Disclaimers and Forward-Looking Statements This presentation and various remarks which may be made during this presentation contain forward-looking statements within the meaning of the Private Securities Litigation Refor

Research Day 2018 Update on Research

Programs June 26, 2018 New York NASDAQ: ALDX Aldeyra Therapeutics, Inc. 2018 Exhibit 99.1

Disclaimers and Forward-Looking

Statements This presentation and various remarks which may be made during this presentation contain forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995 and Section 21E of the Securities Exchange Act

of 1934, as amended, including statements regarding Aldeyra's possible or assumed future results of operations, expenses and financing needs, business strategies and plans, research and development plans or expectations, trends, the structure,

timing and success of Aldeyra's planned or pending clinical trials, expected milestones, market sizing, pricing and reimbursement, competitive position, regulatory matters, industry environment and potential growth opportunities, among other

things. Forward-looking statements include all statements that are not historical facts and, in some cases, can be identified by terms such as "may," "might," "will," "objective," "intend,"

"should," "could," "can," "would," "expect," "believe," "anticipate," "project," "target," "design," "estimate,"

"predict," "potential," "plan" or similar expressions and the negatives of those terms. Forward-looking statements involve known and unknown risks, uncertainties and other factors that may cause Aldeyra's

actual results, performance or achievements to be materially different from any future results, performance or achievements expressed or implied by the forward-looking statements. These statements reflect Aldeyra's current views with respect

to future events and are based on assumptions and subject to risks and uncertainties, including the development, clinical and regulatory plans or expectations for Aldeyra's product candidates and Aldeyra's continuing review and quality

control analysis of clinical data. Important factors that could cause actual results to differ materially from those reflected in Aldeyra's forward-looking statements are described in Aldeyra's most recent Annual Report on Form 10-K and

Quarterly Report on Form 10-Q, as well as Aldeyra's subsequent filings with the Securities and Exchange Commission. All of Aldeyra's development timelines may be subject to adjustment depending on recruitment rate, regulatory review,

preclinical and clinical results, and other factors that could delay the initiation, completion, or reporting of clinical trials. In addition to the risks described above and in Aldeyra's other filings with the SEC, other unknown or unpredictable

factors also could affect Aldeyra's results. No forward-looking statements can be guaranteed and actual results may differ materially from such statements. The information in this presentation is provided only as of June 26, 2018, and Aldeyra

undertakes no obligation to update any forward-looking statements contained in this presentation on account of new information, future events, or otherwise, except as required by law.

Our Mission Developing Next-Generation

Medicines to Improve the Lives of Patients with Immune-Mediated Diseases ~7% Of Western Society Suffer from some form of immune-mediated disease Disease control elusive despite existing therapies, and thus novel approaches are needed Unmet Needs

Source: Shurin and Smolkin, Advances in Experimental Medicines and Biology 601:3-12, 2007; Kuek et al, Postgraduate Medical Journal 83(978): 251-260, 2007.

Developing Next-Generation Medicines to

Improve the Lives of Patients with Immune-Mediated Diseases Deep and Innovative Pipeline focused on immune-mediated diseases Near-Term Development Catalysts support path to commercialization Solid Track Record of development success Solid Cash

Position $ Large Market Potential of late-stage pipeline Cash, cash equivalents and marketable securities were $38.9 million as of March 31, 2018

Reproxalap: Lead Candidate With

Significant Commercial Potential Ocular Inflammation Inborn Errors of Metabolism Dry Eye Disease Allergic Conjunctivitis Noninfectious Anterior Uveitis Sj gren-Larsson Syndrome Potential Competitive Advantages2 Rapid onset, broader activity

Non-drying, durable activity, responder superiority vs. vehicle No expected risk of glaucoma or other corticosteroid toxicities Clinically demonstrated efficacy No FDA therapy currently approved Estimated U.S. Population1 150,000 flares per yr. 30

million 1,0003 20 million Reproxalap Development Stage Phase 2b Phase 3 Phase 3 Phase 3 1 Aldeyra estimates based on internal market research and publicly available information. 2 Pending clinical data, regulatory discussions, payor negotiations,

competition, potential legislative changes, and other factors, which may not be in Aldeyra's control. Preliminary assumptions are subject to change. 3 Extrapolated from a Swedish estimate and a U.S. genetic mutation analysis, it is generally

assumed that there are approximately 1,000 Sj gren-Larsson Syndrome (SLS) patients in the United States and a greater number of SLS patients in Europe.

Deep and Innovative Pipeline Not

Disclosed Reproxalap Ocular Reproxalap Dermal ADX-629 Systemic ADX-103 ADX-1612 Dry Eye Disease Allergic Conjunctivitis Noninfectious Anterior Uveitis Sj gren-Larsson Syndrome Autoimmune Disease Retinal Disease Lymphoproliferative Immune

Disease Phase 2b results H2-2018 Phase 3 results H2-2018 / 2019 Phase 3 results 2019 Phase 3, Part 1 results 2019 Systemic Inflammatory Disease RASP Inhibitors Hsp90 Inhibitors Anti-Inflammatory Ovarian Cancer Mesothelioma Investigator Sponsored

Trial ADX-1615 Autoimmune Disease Cancer Not Disclosed Ocular Inflammation Research Collaboration Investigator Sponsored Trial Indication Compound Approach = Positive Phase 2 clinical data reported in 2016 - 2017

RASP = Reactive Aldehydes Species that are Pro-inflammatory Preclinical Phase 1 Phase 2 Phase 3 Next Expected Milestone Research Program Update Phase 2 results H2-2018

2018 Progress and Near-Term Development

Catalysts Support Path to Commercialization Initiated reproxalap Phase 2b clinical trial in dry eye disease First patient enrolled in reproxalap Phase 3, Part 1 clinical trial in Sj gren-Larsson Syndrome Q3 2018 Reproxalap dry eye disease Phase

2b clinical trial results H2-2018 Reproxalap allergic conjunctivitis Phase 3 results H2-2018/early 2019 Reproxalap noninfectious anterior uveitis Phase 3 clinical trial results 2019 Reproxalap Sj gren-Larsson Syndrome Phase 3, Part 1 clinical

trial results 2019 H1 2018 H2 2018 2019 Initiated reproxalap Phase 3 clinical trial in allergic conjunctivitis Entered into research collaboration with Johnson & Johnson Innovation in systemic inflammatory diseases Disclosed in-license of a

Hsp90 inhibitor Contingent on funding, regulatory review, and other factors. Anticipated Milestones Clinical sites initiated for reproxalap Phase 3, Part 1 clinical trial in Sj gren-Larsson Syndrome

Research Day 2018 Update on Research

Programs June 26, 2018 New York NASDAQ: ALDX

Developing Next-Generation Medicines to

Improve the Lives of Patients with Immune-Mediated Diseases Targeting RASP Targeting Hsp90 Partnership Update ADX-629 for Systemic Immune-Mediated Diseases ADX-103 for Inflammatory Retinal Disease ADX-1612 for Lymphoproliferative Immune Disease and

Cancer ADX-1615 for Autoimmune Disease and Cancer J&J Innovation

Immune System Balance is Complex

Stimulation Regulation Immune Balance Healthy Stimulation Imbalance Autoimmune Disease Regulation Imbalance Cancer

Novel Approaches to Address

Immune-Mediated Disease RASP = Reactive Aldehydes Species that are Pro-inflammatory RASP Activated Cell Cell Proliferation Immune Cell Stimulus Hsp90 Inhibitors RASP Inhibitors

Targeting RASP for Systemic

Immune-Mediated Diseases ADX-629

Targeting RASP: Mediators of

Inflammation and Activators of the Immune System Thiol / Amine Adduct Formation Receptor / kinase, lipid modification Inflammasome, NF B activation; cytokine release Scavenger Receptor A binding Auto-antibody formation RASP Activated Immune

Cell Inflammation Scientific Literature Cardiovasc Res. 2010 Nov 1;88(2):352-9. HNE-induced 5-LO expression is regulated by NF-kB/ERK and Sp1/p38 MAPK pathways via EGF receptor in murine macrophages. Biofactors. 2005;24(1-4):229-36.

Role of 4-hydroxy-2,3-nonenal in the pathogenesis of fibrosis. Cell Mol Biol Lett. 2015 Dec;20(4):647-62. The advanced lipoxidation end product precursor malondialdehyde induces IL-17E expression and skews lymphocytes to the th17

subset. J Leukoc Biol. 2012 Nov;92(5):1055-67. Proinflammatory effects of malondialdehyde in lymphocytes. Diabetes. 2008 Apr;57(4):879-88. Proinflammatory effects of advanced lipoxidation end products in

monocytes. RASP = Reactive Aldehydes Species that are Pro-inflammatory

ADX-629: A Novel Pre-Clinical RASP

Inhibitor for Treatment of Systemic Immune-Mediated Disorders Highly prevalent disease characterized by liver inflammation, fibrosis, cirrhosis, and hepatocellular carcinoma No FDA-approved therapy RASP end-products observed in NASH Over one million

patients in the U.S. suffer from Ulcerative Colitis and Crohn's Disease Chronic autoimmune disease with variable response to therapy RASP observed in preclinical models; decreased RASP metabolism observed in diseased human intestinal tissue

Source: Prevalence data from U.S. Centers for Disease Control and Prevention NASH (non-alcoholic steatohepatitis) IBD (inflammatory bowel disease)

Normal hepatocyte Fatty hepatocyte

Fatty & injured hepatocyte Apoptotic hepatocyte NASH Pathogenesis: Chronic Progression of Inflammation and Fibrosis Adapted from Diehl and Day NEMJ 377:2062-2072, 2017; RASP activity as shown based on published literature and Aldeyra data on

file. RASP-Mediated RASP-Mediated Inflammation Fibrosis

Environmental factors Microorganisms

Diet Infections Stress NSAIDs Appendectomy Smoking Antibiotics Genetic factors Antimicrobial peptides Autophagy Handling of bacteria Chemokines Cytokines Initiating triggers Phase I: Pre-disease stage Phase II: Acute intestinal inflammation Phase

III: Recurrent inflammation Phase IV: Tissue destruction and complications IBD Pathogenesis: Chronic Relapsing Intestinal Inflammation Adapted from Neurath, Nature Reviews Immunology 14:329 - 342, 2014; RASP activity as shown based on

published literature and Aldeyra data on file. RASP- Mediated RASP- Mediated RASP- Mediated Intestinal wall

ADX-629: A Pre-Clinical Novel RASP

Inhibitor ADX-629 is an analog of reproxalap Reproxalap has demonstrated activity in immune-mediated diseases Pre-Clinical Models Sepsis Inflammatory pain Oral mucositis Allergic dermatitis Contact dermatitis Acute lung injury Corneal fibrosis

Clinical Trials Dry eye disease Allergic conjunctivitis Noninfectious anterior uveitis Supporting scientific posters and presentations available on Aldeyra's investors page at ir.aldeyra.com.

ADX-629 Decreased LPS-Induced

Pro-inflammatory Cytokine Levels and Increased Levels of an Anti-inflammatory Cytokine in Animal Models Cytokine Decrease RANTES 93.8% MIP-1 93.1% IL-12(p40) 92.4% G-CSF 91.1% LIF 85.8% MIG 83.3% IL-5 82.3% IL-17 77.4% M-CSF 75.1% GM-CSF 73.7%

IL-13 73.6% IL-15 72.1% Cytokine Decrease IL-15 72.1% IL-9 72.0% IL-1 71.5% IFN 71.3% IL-12(p70) 68.8% IL-1 67.5% IL-7 65.2% LIX 62.0% TNF 60.3% IL-3 56.0% VEGF 55.2% Eotaxin 26.1 % Cytokine Increase IL-10 2103% ADX-629 (100

mg/kg) was administered intraperitoneally to mice LPS was administered intraperitoneally (1 mg/kg) 15 minutes later Blood was collected 2 hours after ADX-629 administration and plasma cytokines measured by ELISA p values range from < 0.05 to <

0.0001 Pro-Inflammatory Anti-Inflammatory

Planning to initiate clinical

testing in 2019 Potential ADX-629 Development Overview 2018 2020 Today 144 days Jul 17 - Feb 1 106 days Feb 1 - Jun 30 155 days Jul 1 - Jan 31 155 days Jul 1 - Jan 31 Contingent on pre-clinical studies, clinical trials, funding, regulatory review,

and other factors. Phase 2a IBD Clinical Trial Phase 2a NASH Clinical Trial IND-Enabling Toxicology Phase 1 Clinical Trial

Targeting RASP for Inflammatory

Retinal Disease ADX-103

ADX-103: A Structurally Distinct

Pre-Clinical RASP Inhibitor Potential product candidate for treatment of retinal disease RASP observed in retinal disease Efficacy in several preclinical models of ocular inflammation Diabetic macular edema (DME) Dry age-related macular degeneration

(AMD) / Stargardt's Disease Posterior uveitis DME: Glyoxal, methylglyoxal, allysine AMD/Stargardt's Disease: Retinaldehyde Posterior uveitis: Malondialdehyde, 4-hydroxynonenal

Diabetic Macular Edema: ADX-103

Blocked Diabetes-Induced Retinal Changes in Animal Models Male Norway rats were administered streptozotocin (STZ), 55 mg/kg IP, on Day 0 to induce diabetes Two single doses of ADX-103 (17.5 g each) were administered intravitreally, after

induction of diabetes (Days 42 and 57) Histopathology of the retina was conducted at Day 71 Scale: 1 = minimal microscopically visible changes 2 = mild microscopically visible changes 3 = moderate microscopically visible changes Retinal Thickness

Changes at Day 71 Presented at the 2018 ARVO annual meeting.

Endotoxin-Induced Uveitis: ADX-103

Decreased Ocular Inflammation in Animal Models Ocular inflammation in rats induced by footpad injection of a bacterial endotoxin (LPS) Severe model Peaks at 24 hours A single intravitreal dose of ADX-103 (25 g/eye) was administered at hour 1

post-LPS administration Retina-choroid complex was scored for inflammatory changes at six and 24 hours Presented at the 2018 ARVO annual meeting. *p < 0.05; **p < 0.01 Retinal Inflammation at 6 Hrs. Post Insult Retinal Inflammation at 24 Hrs.

Planning to initiate clinical

testing in 2019 Potential ADX-103 Retina Program Overview 2018 2020 Today 144 days Jul 17 - Feb 1 106 days Feb 1 - Jun 30 155 days Jul 1 - Jan 31 155 days Jul 1 - Jan 31 Phase 2 Clinical Trial IND-Enabling Toxicology Phase 1/2 Clinical Trial

Contingent on pre-clinical studies, clinical trials, funding, regulatory review, and other factors.

Lymphoproliferative Immune Disease and Cancer ADX-1612

ADX-1612: Clinically Advanced Asset

With Extensive Preclinical, Nonclinical, and Clinical Data In-licensed for its potential in immune-mediated disease ADX-1612 clinically-tested in oncology as ganetespib Preclinical efficacy in immune disorders Unregulated proliferation of immune

cells Lymphoproliferative/immunoproliferative disorders Hyperactive immune system IV formulation Ongoing Investigator-Sponsored Trials (ISTs) using ADX-1612 in combination with platins

ADX-1612: Expanding The Potential

Repertoire for Treatment of Immune-Mediated Diseases Adapted from Tukaj and Wegrzyn Cell Stress and Chaperones 21:213 - 218, 2016. Cytoplasm Nucleus ADX-1612 ADX-1612 Hsp90 Hsp90 Hsp70 NF B Inflammation HSF1 HSE mRNA hsp70 ADX-1612 Hsp90

inhibitor Hsp90 Upregulated in stressful conditions Role in antigen presentation in dendritic cells Client proteins involved in signal transduction and cell cycle (e.g., cell proliferation, survival, apoptosis) Inhibition of Hsp90 Prevents proper

folding of client proteins, leading to degradation and disruption of cell cycle Prevents DNA repair