NASDAQ: SNGX Rising to the Challenges of Rare Disease Treatment Forward - Looking Statements This presentation contains forward - looking statements . All statements other than statements of historical facts contained in

NASDAQ: SNGX Rising to the Challenges of Rare Disease Treatment

Forward - Looking Statements This presentation contains forward - looking statements . All statements other than statements of historical facts contained in this presentation, including statements regarding our future results of operations and financial position, business strategy, prospective products and product candidates and their development, regulatory approvals, ability to commercialize our products and product candidates and attract collaborators, reimbursement for our product candidates, research and development costs, timing and likelihood of success, plans and objectives of management for future operations, our ability to obtain and maintain intellectual property protection for our product candidates and their development, competing therapies, and future results of current and anticipated products and product candidates, are forward - looking statements . These statements involve known and unknown risks, uncertainties, and other important factors that may cause our actual results, performance or achievements to be materially different from any future results, performance or achievements expressed or implied by the forward - looking statements, many of which are disclosed in detail in our reports and other documents filed with the Securities and Exchange Commission . Because forward - looking statements are inherently subject to risks and uncertainties, some of which cannot be predicted or quantified and some of which are beyond our control, you should not rely on these forward - looking statements as predictions of future events . The events and circumstances reflected in our forward - looking statements may not be achieved or occur and actual results could differ materially from those projected in the forward - looking statements . Except as required by applicable law, we do not plan to publically update or revise any forward - looking statements contained herein, whether as a result of any new information, future events, changed circumstances, or otherwise . Certain information contained in this presentation and statements made orally during this presentation relate to or are based on studies, publications, surveys and other data obtained from third - party sources . In addition, no independent source has evaluated the reasonableness or accuracy of Soligenix, Inc . internal estimates and no reliance should be made on any information or statements made in this presentation relating to or based on such internal estimates . 2

Company Highlights 3 Diversified product portfolio in advanced development , targeting rare disease indications in inflammation, oncology and biodefense with $200M+ markets worldwide o Phase 3 clinical program for the treatment of cutaneous T - cell l ymphoma ( SGX301) - Orphan drug, fast track and promising innovative medicine (UK) designations - Pivotal study actively enrolling patients with results second half 2017 o Phase 3 clinical program for the treatment of oral mucositis in head & neck cancer (SGX942) - Fast track and promising innovative medicine (UK) designations - Pivotal study to begin first half 2017 with results second half 2018 o Phase 3 clinical program for the treatment of pediatric Crohn's disease ( SGX203 ) - Orphan drug and fast track designations - Pivotal study to begin second half 2017 with results second half 2019 Robust news flow potential over next 24 months across multiple development programs Collaborations established with biotech, academia and government agencies Development candidates supported in whole or in part by non - dilutive contract/grant funding provided by the government, including o NIAID contract award of up to $24.7M supporting the development of RiVax for pre - exposure to ricin toxin

4 Rare Disease Pipeline Product Candidates Preclinical Phase 1 Phase 2 Phase 3 Market SGX301 Cutaneous T - Cell Lymphoma (CTCL) SGX942 Oral Mucositis in Head & Neck Cancer** SGX203 Pediatric Crohn's Disease** SGX201 Radiation Enteritis** BioTherapeutics Vaccines / BioDefense** Product Candidates (FDA Animal Rule) Proof - of - Concept Animal Phase 1 Phase 2/3 Market ThermoVax ( TVax ) Heat Stabilization Technology for Vaccines RiVax TM + TVax - Heat Stable Vaccine Ricin Toxin Pre - Exposure OrbeShield - Therapeutic GI Acute Radiation Syndrome (GI ARS) SGX943 - Therapeutic Melioidosis Ph. 3 data 2H 2018* Anticipated event and timing * Potential value drivers dependent on continued government funding and/or other funding sources Ph . 3 data 2H 2019 Positive Phase 1/2 data Denotes funding in whole or in part by NIH, BARDA and/or FDA NIAID Contract Award of up to $24.7M BARDA and NIAID Contract Awards of $18M collectively Ebola Vaccine Collaboration; positive proof of concept preclinical data NIH Small Business Grant Award of $300,000; positive proof of concept preclinical data Enrolling ; Ph. 3 data 2H 2017 ORPHAN & FAST TRACK DESIGNATIONS FAST TRACK DESIGNATION FAST TRACK DESIGNATION FAST TRACK ORPHAN DESIGNATION VACCINE PLATFORM ORPHAN & FAST TRACK DESIGNATION ORPHAN & FAST TRACK DESIGNATIONS

2 H : Ph. 1/2 human safety data 1H : Ph. 1/2 human safety study start 5 Multiple Potential Value Drivers SGX203* ThermoVax * 2016 SGX301 2017 RiVax TM * OrbeShield * 2018 2H : Ph. 3 start Pediatric Crohn's SGX942* Positive Ph. 2 data in Oral Mucositis * Potential value drivers dependent on continued government funding and/or other funding sources Preclinical animal data EU orphan drug designation UK Promising Innovative Medicine 1H : Preclinical animal data FDA clearance Ph. 3 protocol Positive Ebola vaccine data 1H: NDA submission CTCL 1H: Ph. 3 start Oral Mucositis 2H : Preclinical animal data NIAID contract option award 1H : Ricin vaccine animal data 2 H : Ph. 1/2 human safety data 2H: Ph. 3 data CTCL 2H: Ph. 3 data Oral Mucositis

Significant WW Market Potential $300 0 50 100 150 200 $ Millions 250 300 $250 400 350 OrbeShield GI Acute Radiation Syndrome SGX301 Cutaneous T - Cell Lymphoma Assumptions (1) Oral Mucositis in Head and Neck Cancer 90,000 Patients US 90,000 Patients EU Cutaneous T - Cell Lymphoma 20,000 Patients US 20,000 Patients EU Pediatric Crohn's Disease 80,000 Patients US 80,000 Patients EU Acute Radiation Enteritis in Colorectal Cancer 50,000 Patients US 50,000 Patients EU RiVax TM Ricin Vaccine Assumes 3 year procurement order of $200 million OrbeShield GI ARS Assumes 3 year procurement order of $450 million SGX201 Acute Radiation Enteritis $200 6 RiVax TM Ricin Vaccine $200 $450 450 500 $500+ SGX942 Oral Mucositis (1) Supporting data on file SGX203 Pediatric Crohn's Disease

Experienced Management and Board of Directors 7 Christopher J. Schaber , PhD President & CEO 27 years of experience Discovery Laboratories (COO) Acute Therapeutics (Co - Founder) Ohmeda Pharmaceuticals The Liposome Company Wyeth Ayerst Oreola Donini, PhD Chief Scientific Officer 15 years of experience Inimex Pharmaceuticals ESSA Pharma, Inc Kinetek Pharmaceuticals Karen Krumeich Chief Financial Officer Keith Brownlie , CPA 35 years of experience Ernst & Young Gregg Lapointe , CPA, MBA 20 years of experience Cerium Pharmaceuticals (CEO) Sigma - Tau Pharmaceuticals AstenJohnson Price Waterhouse Coopers Robert Rubin , MD 36 years of experience The Lewin Group Georgetown School of Medicine Former Assistant Surgeon General of the United States Jerome Zeldis , MD, PhD 33 years of experience Celgene Corporation (CMO) Sandoz Janssen Research Institute Marco Brughera, DVM 30 years of experience Sigma - Tau SpA (Global Head, Rare Disease Franchise) Pfizer Pharmacia Richard Straube, MD Chief Medical Officer 30 years of experience Stealth Peptides Inc. INO Therapeutics Ohmeda Pharmaceuticals Centocor 25 years of experience Cerecor Mela Sciences Bristol - Myers Squibb

Targeted Approach to Treating Oncology & Inflammation BioTherapeutics 8

BioTherapeutics Business Segment Commercial targets - unmet medical needs in oncology and inflammation 9 BioTherapeutics Product Candidates Preclinical Phase 1 Phase 2 Phase 3 Market SGX301 Cutaneous T - Cell Lymphoma (CTCL) SGX942 Oral Mucositis in Head & Neck Cancer** SGX203 Pediatric Crohn's Disease** SGX201 Radiation Enteritis** ORPHAN & FAST TRACK DESIGNATIONS Enrolling ; Ph. 3 data 2H 2017* FAST TRACK DESIGNATION Ph. 3 data 2H 2018* ORPHAN & FAST TRACK DESIGNATIONS Ph . 3 data 2H 2019* FAST TRACK DESIGNATION Positive Phase 1/2 data Denotes funding in whole or in part by NIH, BARDA and/or FDA *Anticipated event and timing * *Potential value drivers dependent on continued government funding and/or other funding sources

10 Cutaneous T - Cell Lymphoma - Disease Overview Cutaneous T - cell lymphoma (CTCL) o R are class of Non - Hodgkin's Lymphoma (NHL) o Malignant T - cells migrate to the skin o Cancer forms patches or lesions CTCL affects over 40 , 000 NHL patients worldwide ; currently no cure Two main subtypes of CTCL o Mycosis fungoides (MF) - Early - stage (most common), 88% 5 - year survival o S zary syndrome (SS) - Advanced - stage, 24% 5 - year survival No approved front - line therapy for early stage (I - IIA) CTCL (~95% of CTCL patients); unmet medical need Atypical T - cells in dermis

11 SGX301 - Synthetic Hypericin SGX301 is a first - in - class, topical drug applied to CTCL skin lesions followed by activation with safe, visible, fluorescent light to kill malignant T - cells Affects over 40,000 patients annually worldwide No approved front - line therapy for early stage (I - IIA) CTCL (~95% of CTCL patients); unmet medical need Most common (unapproved) therapy used for early - stage disease is psoralen given with ultraviolet A (UVA) light, referred to as PUVA PUVA contains Black Box warning for potential malignancies (melanoma) due to psoralen being mutagenic and light source (UVA) being carcinogenic Market Opportunity Development Status FDA Orphan Drug and Fast Track designations granted UK MHRA Promising Innovative Medicine designation granted Phase 1 study demonstrated safety and tolerability Phase 2 double - blind, placebo - controlled, multi - center study d emonstrated significant (p < 0.04) response Pivotal Phase 3 trial actively enrolling ~120 subjects Results expected 2H 2017

CTCL Patch Pre - Therapy Hypericin Therapy Using Visible Light CTCL Patch Post - Therapy SGX301 - Phase 2 Response Rate 12 Summary of CTCL Lesion Responses to Synthetic Hypericin Ointment Following Six Weeks of Treatment Responders/Total Percent Responders Hypericin Responders 7/12 58.3% Placebo Responder 1/12 8.3% Note : No serious adverse events other than mild phototoxicity at treated site Data Source: Journal American Academy Dermatology, Vol 63, Number 6, 2010

13 Oral Mucositis - Disease Overview Oral mucositis (OM) o Multi - factorial disease linked to a dysregulation of the innate immune system OM affects over 180,000 head and neck (H&N) cancer patients worldwide Debilitating side effect of cancer chemotherapy and / or radiotherapy o Triggering inflammatory cascade o Massive ulceration of the mouth, tongue, soft palate and oropharynx Results in: o Severe pain causing an inability to eat or even drink o Reduced cancer treatment tolerance o Significant increases in resource use and cost of care No approved drug for OM in head and neck cancer; unmet medical need Ref: S. Sonis 2004 Inflammation causes worsening damage Secondary infection

14 SGX942 - Innate Defense Regulator SGX942 (dusquetide) is a first - in - class, injectable drug, called an Innate Defense Regulator (IDR), that modulates the body's innate immune system to reduce inflammation OM affects over 180,000 H&N cancer patients worldwide No approved drug for OM in H&N cancer; unmet medical need Only approved drug for OM is palifermin in transplantation; contra - indicated for patients with solid tumors like H&N cancer Exclusive commercial collaboration with SciClone in China Market Opportunity Development Status FDA Fast Track designation granted UK MHRA Promising Innovative Medicine designation granted Phase 1 study in 84 healthy volunteers demonstrated safety Phase 2 double - blind, placebo - controlled, multi - center study in 111 H&N cancer patients with OM demonstrated significant (p=0.04) response o 50% reduction in duration of severe OM in overall population o 67% reduction in duration of severe OM in highest risk population receiving at least 55 Gy radiation and more aggressive (80 - 100 mg/m 2 every 3 rd week) chemotherapy Pivotal Phase 3 protocol clearance from FDA and EMA with study initiation targeted 1H 2017

0 10 20 30 Duration of Severe Oral Mucositis Overall Population D u r a t i o n W H O 3 M e d i a n 9 5 % C I ( D a y s ) Placebo N=38 SGX942 1.5mg/kg N=36 18 days 9 days p=0.099 50% 0 20 40 60 Duration of Severe Oral Mucositis Aggressive Chemotherapy D u r a t i o n W H O 3 M e d i a n 9 5 % C I ( D a y s ) Placebo N=22 SGX942 1.5mg/kg N=24 30 days 10 days p=0.040 67% SGX942 - Oral Mucositis Results 15 Clinically Meaningful Results demonstrated in the 1.5 mg/kg dose group versus placebo at one month following completion of chemoradiation therapy o Primary Endpoint - Decrease in the duration of severe OM o Primary endpoint outcome consistent with multiple key secondary measures Decrease in incidence and delay in mean onset of severe OM Decrease in duration of ulcerative mucositis Decrease in pain (opioid) medication use Decrease in infection rates Increase in tumor resolution ("complete response") Increase in survival Data Source: Journal of Biotechnology, a vailable online 13 October 2016; http://dx.doi.org/10.1016/j.jbiotec.2016.10.010

SGX942 - Oral Mucositis Results 16 Clinically Meaningful Results demonstrated in SGX942 1.5 mg/kg dose group versus placebo one month following completion of chemoradiation in patients at higher risk for severe OM receiving aggressive chemotherapy (80 - 100 mg/m 2 ) o Relative 22% decrease in duration of ulcerative OM o Relative 70% decrease in percent of patients with residual severe OM o Relative 44% increase in tumor "complete response" at one - month post radiation; sustained through the 12 - month follow - up period o Relative 42% decrease in clinically diagnosed bacterial infection rate o Relative 35% decrease in mortality throughout the follow - up period Data Source: Journal of Biotechnology, a vailable online 13 October 2016; http://dx.doi.org/10.1016/j.jbiotec.2016.10.010 0 20 40 60 80 Duration of Ulcerative Oral Mucositis Aggressive Chemotherapy D u r a t i o n W H O 2 M e d i a n 9 5 % C I ( D a y s ) Placebo N=22 SGX942 1.5mg/kg N=24 65 days 51 days p=0.099 0 20 40 60 80 100 No Tumor Progression at 12 Months Aggressive Chemotherapy % C o m p l e t e R e s o l u t i o n Placebo N=22 SGX942 1.5mg/kg N=24 64% 82%

17 Pediatric Crohn's Disease - Disease Overview Pediatric Crohn's disease o Chronic inflammatory disorder of the gastrointestinal (GI) tract o Diarrhea, rectal bleeding and abdominal pain Resulting in growth failure, malnutrition, pubertal delay and bone demineralization Over 160,000 children/adolescents with Crohn's disease worldwide Location of disease o Adult predominantly lower GI tract o 50% of children have involvement in the upper GI tract No approved drug for mild - to - moderate pediatric Crohn's disease in the US; unmet medical need Normal mucosa under endoscopy

18 SGX203 - Beclomethasone Dipropionate SGX203 is a proprietary oral formulation of immediate and delayed release beclomethasone 17,21 - dipropionate (BDP) tablets to treat GI inflammation with less toxicity than the current standard systemic steroid therapy 160,000 children/adolescents with Crohn's disease worldwide - 50% have inflammation of upper GI No approved drug for mild - to - moderate; unmet medical need Currently unapproved systemic steroids used front - line cause adrenal suppression, growth impairment, bone demineralization Oral BDP delivers high GI steroid effects with minimal (~35%) systemic side effects Remicade and Humira only approved products in Pediatric Crohn's in US - generally used after steroids fail Both contain Black Box warning for increased risk of infection and potential malignancy (T cell lymphoma) Market Opportunity Development Status FDA Orphan Drug and Fast Track designations granted Active ingredient BDP FDA approved for over 40 years in other delivery forms (e.g., aerosol) to treat diseases such as asthma ~350 subjects treated with oral BDP to date in multiple trials Pivotal Phase 3 adaptive trial in ~150 subjects targeted 2H 2017 Results expected 2H 2019

Vaccine/BioDefense 19 Addressing Critical Concerns for Industry and Government

20 Vaccine/BioDefense Business Segment Vaccines / BioDefense** Product Candidates (FDA Animal Rule) Proof - of - Concept Animal Phase 1 Phase 2/3 Market ThermoVax ( TVax ) Heat Stabilization Technology for Vaccines RiVax TM + TVax - Heat Stable Vaccine Ricin Toxin Pre - Exposure OrbeShield - Therapeutic GI Acute Radiation Syndrome (GI ARS) SGX943 - Therapeutic Melioidosis Ebola Vaccine Collaboration; positive proof of concept preclinical data NIH Small Business Grant Award of $300,000; positive proof of concept preclinical data FAST TRACK ORPHAN DESIGNATION VACCINE PLATFORM ORPHAN & FAST TRACK DESIGNATION Denotes funding in whole or in part by NIH, BARDA and/or FDA *Anticipated event and timing * *Potential value drivers dependent on continued government funding and/or other funding sources Funded by Government - Medical Countermeasures for Civilian and Military Use NIAID Contract Award of up to $24.7M BARDA and NIAID Contract Awards of $18M collectively

ThermoVax - Vaccine Thermostability Platform 21 ThermoVax is a proprietary freeze - drying process that enables vaccines to be stored without refrigeration Demonstrated retained efficacy up to 1 year at 40 C (104 F) Market Opportunity Development Status WHO reports about 50% of all vaccine doses globally are wasted due to excursions from required cold chain temperature ranges DHHS reports vulnerabilities in pediatric vaccine programs due to undetected cold chain variations Elimination of cold chain costs would significantly increase profit potential of vaccines, especially in third - world/emerging markets Continue development under $24.7M NIAID contract for RiVax Conduct POC feasibility studies with other adjuvanted vaccines including secondary adjuvants and/or multivalent combinations ThermoVax stabilized Ebola protein antigen at 40 C Positive results: o Ricin vaccine o Anthrax vaccine o HPV vaccine 0 7 30 90 180270360 0 50 100 Stability Day % I m m u n o g e n i c i t y 40 o C ThermoVax 40 o C Original

22 Heat - stable ricin vaccine provided 100% protection in a non - human primate aerosol challenge model (right) Demonstrated safety in Phase 1 studies Market Opportunity Development Status Ricin toxin vaccine of rising interest to US due to recent terrorist threats and ease of castor bean procurement and production Government has placed priority on development activities Potential to be first approved ricin toxin vaccine FDA Orphan Drug designation granted Development agreement with Emergent BioSolutions for manufacturing NIAID contract award of up to $24.7M over 6 years RiVax TM - Ricin Toxin Vaccine Days Post-Intoxication % S u r v i v a l 0 5 10 15 0 25 50 75 100 Sham (N=6) Vaccine (N=12) p<0.0001 *Late death not directly attributed to ricin intoxication

23 Two - tablet BDP system also efficacious in animal models of gastrointestinal acute radiation syndrome (GI ARS) Preliminary proof of concept data in canine model of GI ARS (right) Market Opportunity Development Status Oral BDP is a "re - purposed" drug, of particular importance to BARDA Category A countermeasures against radiation exposure of interest to US / World governments Over $600M spent to date on therapeutics against radiation injury FDA Orphan Drug and Fast Track designations granted BARDA and NIAID contract awards of $18M collectively Pursue additional grants/contracts to support development OrbeShield for GI Acute Radiation Syndrome 0 5 10 15 0 25 50 75 100 Study Day % S u r v i v a l p<0.05 Placebo (N=4) BDP (N=6)

Investment Highlights 24 Diversified product portfolio in advanced development , targeting rare disease indications in inflammation, oncology and biodefense with $200M+ markets worldwide o Phase 3 clinical program for the treatment of cutaneous T - cell l ymphoma ( SGX301) - Orphan drug, fast track and promising innovative medicine (UK) designations - Pivotal study actively enrolling patients with results second half 2017 o Phase 3 clinical program for the treatment of oral mucositis in head & neck cancer (SGX942) - Fast track and promising innovative medicine (UK) designations - Pivotal study to begin first half 2017 with results second half 2018 o Phase 3 clinical program for the treatment of pediatric Crohn's disease ( SGX203 ) - Orphan drug and fast track designations - Pivotal study to begin second half 2017 with results second half 2019 Robust news flow potential over next 24 months across multiple development programs Collaborations established with biotech, academia and government agencies Development candidates supported in whole or in part by non - dilutive contract/grant funding provided by the government, including o NIAID contract award of up to $24.7M supporting the development of RiVax for pre - exposure to ricin toxin

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