This presentation contains certain forward looking information about ZIOPHARM Oncology that is intended to be covered by the safe harbor for forward looking statements provided by the Private Securities Litigation Reform

(NYSE: XON) Financial Highlights 19 Ad RTS IL 12 advancing through Phase 2 studies in breast cancer and melanoma On mechanism and on target response and toxicity observed Expanded data anticipated in late 2014 and in 2015 Pre clinical/clinical data on glioblastoma in 2014 Poised to launch multiple new studies in 2014 and beyond INDs targeting new gene expression patterns, new cell types and new indications ZIOPHARM Oncology 20 www.ziopharm.com NASDAQ: ZIOP Jonathan Lewis, MD, PhD Chief Executive Officer The Future of Cancer Therapy

Larry Norton, M.D., Deputy Physician in Chief for Breast Cancer Programs, Memorial Sloan Kettering Cancer Center Clinical Conclusions to Date 12 Significant Market Potential for Ad RTS IL 12 13 GBM Phase 1 dose escalation study IL 12 Next Study Timelines 14 Melanoma Phase 2 combination study with SOC Breast cancer Phase 2 combination study with SOC FPI 1H 2014 Preliminary data YE 2014 FPI 1H 2014 Preliminary data YE 2014 FPI 1H 2014 Preliminary data 1H 2015 A Growing Oncology Portfolio Compound Pre Clinical Phase 1 Phase 2 Ad RTS IL 12 IND Melanoma Breast GBM Cell based programs Cell signal targeting Multigenic platforms Immunotherapy Programs 15 We can intelligently and intentionally construct multi gene therapies 16 Human mesenchymal stem cells (hMSCs) genetically modified with multigenic hIL 12, hIFN a , and CTLA4 decoy Potential use of hMSCs for tumor targeted delivery of multiple RTS regulated cancer immunotherapies Integration of modularized protein engineering technology and the RTS platform to develop high affinity trastuzumab (Herceptin ) and cetuximab (Erbitux ) single chain variable fragment Fc proteins for gene therapy Potential use of inducible multigenic systems to treat cancer using multigenic therapeutic antibodies RTS regulated immunomodulatory proteins expressed from multigenic embedded cellular bioreactor (ECB) using electroporation into skeletal muscle Potential use of ECBs to deliver multiple proteins systemically, under control of RTS platform Combination Therapies Targeting Multiple Cancers: Potential INDs 17 Upcoming Milestones 18 Program Milestone Timing IL 12 Phase 2 breast cancer study data 2014 Phase 2 advanced melanoma study data 2014 Initiate Phase 1/2 glioblastoma multiforme study 1H 2014 Initiate Phase 2 melanoma combo study 1H 2014 Initiate Phase 2 breast cancer combo study 1H 2014 New Indications Report discovery and preclinical data 2014 Submit INDs for monogenic/multigenic studies 2H 2014 and beyond Publications and Presentations Across programs 2014 Corporate Seek partnering opportunities Ongoing Approx. 100 million shares outstanding (pro forma) Approx. $77.4 million in cash and investments (pro forma) No debt Channel partner/top shareholder Intrexon Corp.

Molecular and Cellular Oncology DNA Coded Toolset 4 Controlled Expression and Delivery of Therapeutic Proteins with RheoSwitch : This is the most advanced clinical method to turn genes on and off The Power of Intrexon s RheoSwitch Technology Local High Potency Monogenic/Multigenic Dose control Orally activated biologic on/off switch 5 IL 12 Production is Modulated by Veledimex (Activator Ligand) in HT 1080 Cells 6 Veledimex Tightly and Precisely Controls the Expression of IL 12 mRNA in the Tumor 7 CD8+ CD45RO+ Cytotoxic T Cells Memory T Cells (TILs) Significantly Increase in Tumors Following Ad RTS IL 12 Treatment Images were obtained using an Aperio ScanScope XT whole slide imager and digitized at 20x. 8 Subjects with unresectable stage III/IV melanoma, n=13 (Phase 1) + n= 8 (Phase 2, ongoing) Intratumoral injection of Ad RTS hIL 12 on Day 1 of each cycle Oral administration of veledimex to activate gene expression of hIL 12 Phase 1/2 Melanoma Study 9 Primary Objective Evaluate the safety and tolerability of intratumoral injections of Ad RTS hIL 12 in combination with veledimex Secondary Objective Inform the selection of a veledimex dose and regimen for further study in combination with Ad RTS hIL 12 Initial increase in lesion size due to immune response seen at Cycle 1 Day 16 Lesion was undetectable at Cycle 2 Day 1 Subject ultimately progressed and was taken off study Prominent Tumor Infiltrating Lymphocyte Response Correlates with Biologic Activity C1D1 C1D16 C2D1 10 Kaplan Meier Survival in GL261 Orthotopic Syngeneic Mouse Glioma Model Glioblastoma Multiforme: IL 12 Preclinical Activity 11 Veledimex (AL) dosing Day 4 to EOS at ~ 675 mg/m2/day in chow; DC RTS IL 12 or Ad RTS IL 12 on Day 5 100% survival observed with Ad RTS IL 12 + AL or DC RTS IL 12 + veledimex Tight control of expression and biologic activity High expression of IL 12 mRNA in tumors, tightly controlled by veledimex dose Increased tumor infiltrating lymphocytes (TILs) observed in the tumor microenvironment, suggesting multiple favorable biologic effects of IL 12 expression On mechanism and on target response and toxicity Melanoma : potent biologic activity in injected and non injected lesions Breast : on mechanism and on target toxicity demonstrates powerful manifestation of the immune system controlled by dose dependent inducible expression of IL 12 Adverse events consistent with immunotherapy use and immune response; Serious adverse events reversed after veledimex dosing stopped Optimization of dose and scheduling to refine response and tolerability is ongoing This opens the possibility that, for the first time, we can achieve personalized scheduling as a component of personalized cancer medicine.

(NYSE: XON) Phase 2 program: Ad RTS IL 12 High intratumoral expression of IL 12 Targeting multiple cancers, including melanoma, breast cancer and glioma Multiple new clinical studies planned through 2015 Technology platform driving clinical program Enabling multigenic approach to immunotherapy and cancer therapy Multiple INDs planned through 2015 ZIOPHARM Today 2 Synthetic DNA enables: creation of new therapies with targeted biofunction precise control of biologic concentration and dosing better therapeutic index through controlled protein delivery and cellular targeting economically feasible approach to combination biologic therapies Why Focus on Synthetic DNA Based Medicine? 3 Synthetic DNA is DNA that is intelligently and intentionally designed for a specific function.

Our audience is cautioned not to place undue reliance on these forward looking statements that speak only as of the date hereof, and we do not undertake any obligation to revise and disseminate forward looking statements to reflect events or circumstances after the date hereof, or to reflect the occurrence of or non occurrence of any events. Forward Looking Statements 1 Clinical stage, synthetic biology oncology company Gene based therapies regulating protein expression and controlling cellular function Clear leader in in vivo control of gene regulation and expression Technology channel partner Intrexon Corp.

Food and Drug Administration or equivalent foreign regulatory agencies and for which indications; whether any of our therapeutic candidates will be successfully marketed if approved; whether our DNA based biotherapeutics discovery and development efforts will be successful; our ability to achieve the results contemplated by our collaboration agreements; the strength and enforceability of our intellectual property rights; competition from pharmaceutical and biotechnology companies; the development of and our ability to take advantage of the market for DNA based biotherapeutics; our ability to raise additional capital to fund our operations on terms acceptable to us; general economic conditions; and the other risk factors contained in our periodic and interim reports filed with the SEC including, but not limited to, our Annual Report on Form 10 K for the fiscal year ended December 31, 2012, and our Quarterly Report on Form 10 Q for the fiscal quarter ended June 30, 2013.

All of such statements are subject to certain risks and uncertainties, many of which are difficult to predict and generally beyond the control of the Company, that could cause actual results to differ materially from those expressed in, or implied or projected by, the forward looking information and statements. These risks and uncertainties include, but are not limited to: whether any of our therapeutic candidates will advance further in the clinical trials process and whether and when, if at all, they will receive final approval from the U.S.

Forward looking statements are statements that are not historical facts. Words such as expect(s), feel(s), believe(s), will, may, anticipate(s) and similar expressions are intended to identify forward looking statements. These statements include, but are not limited to, statements regarding our ability to successfully develop and commercialize our therapeutic products, our ability to expand our long term business opportunities; financial projections and estimates and their underlying assumptions; and future performance.

www.ziopharm.com J.P. Morgan 32nd Annual Healthcare Conference January 2014 Jonathan Lewis, MD, PhD Chief Executive Officer The Future of Cancer Therapy Exhibit 99.1 This presentation contains certain forward looking information about ZIOPHARM Oncology that is intended to be covered by the safe harbor for forward looking statements provided by the Private Securities Litigation Reform Act of 1995, as amended.