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 18 We understand the biologic basis of cancer and how to engineer new products We have the ability to deliver DNA and stimulate a controlled therapeutic immune response Clinical testing is validating our vision Intrexon partnership is enabling expansion of our pipeline Big pharma is very interested in our approach We have the potential to radically change the economics of cancer treatment Our financial success will be driven by multiple products and collaborations, not one or two Why Invest in ZIOPHARM?

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 Immuno Oncology company Focus on treatment through DNA expression and cell control Phase 1/2 program targeting melanoma, breast cancer and glioma Intrexon partnership enabling potential paradigm shift New INDs through 2015 exploring multigenic approach to cancer treatment ZIOPHARM Today 2 DNA synthesis and delivery enable: creation of new therapies which target cancer cells precise control of biologic concentration and dosing better therapeutic index through controlled protein delivery and cellular targeting economically feasible approach biologic therapies and Immuno Oncology Why Focus on DNA Based Medicine? 3 ZIOP: translational medicine and oncology drug development XON: synthetic biology platform enabling DNA delivery and control Exclusive channel partner agreement for the treatment of all human cancer: ZIOP responsible for product development and commercialization XON responsible for manufacturing, process improvement R D, patents 50:50 revenue/net profit split Current targets: melanoma, breast cancer, glioma, other cancers Intrexon Collaboration: Leveraging Our Assets Page 4 We Have the Tools to Treat Cancer Better 5 Cytokines mAb scFv scFv toxin Systemic decoy Intracellular decoy Metabolic Enzyme RNA Protein Ligand DC T Cell B Cell Macrophage NK cell Treg Other immune cells Immune Cells Direct tumor lysis ADCC Complement cytotoxicity Innate immunity stimulation Adaptive immunity stimulation Immune evasion inhibition Pro apoptosis Necrosis Anti angiogenesis Growth inhibition Anti tumor metabolism EMT blockade Non immune Cells Effectors Cells Anti tumor function Tumor and microenvironment MSC Epithelial Endothelial Tumor Cell Skeletal Muscle Controlled Expression and Delivery of Therapeutic Proteins with Intrexon s RheoSwitch : This is the most advanced clinical method to turn genes on and off The Power of RheoSwitch Technology High Potency Monogenic/Multigenic Dose control Orally activated biologic on/off switch Gene Expression RheoSwitch 6 Ad RTS IL 12: Solving the Problem of Serum Concentration Page 7 rIL 12 = recombinant IL 12 hIL 12 = Ad RTS IL 12 Atkins, MB et al Clin Cancer Res 1997;3:409 417 11137 3530 27 14 0 2000 4000 6000 8000 10000 12000 rIL 12 hIL 12 IL 12 Production is Modulated by Veledimex (Activator Ligand) in HT 1080 Cells 8 OFF OFF ON 1 9 19 29 39 49 59 0 6 12 18 24 30 36 42 48 54 60 66 72 78 84 90 Time after viral transduction (hours) Oral Veledimex Tightly and Precisely Controls the Expression of IL 12 mRNA in the Tumor 9 Veledimex Dose n=7 OFF OFF ON 0.1 1 10 100 1000 10000 100000 1000000 Baseline Maximum D1 D7 7 Days Post treatment 100 mg 160 mg 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. 10 On Off CD8+ CD45RO+ Systemic Immune Activity: Patterns of Anti Tumor Response Patient# 1 3 2 Page 11 75 50 25 0 25 50 High expression of IL 12 mRNA in tumors, tightly controlled by veledimex dose Clinical Observations to Date 12 We can control gene expression to achieve a desirable immune response We have seen potent systemic biologic activity and reversible toxicity Melanoma: potent biologic activity in injected and non injected lesions Breast: on mechanism and on target toxicity demonstrates powerful immune response controlled by dose dependent expression of IL 12 Adverse events consistent with immunotherapy use and immune response; serious adverse events reversed after veledimex dosing stopped Increased tumor infiltrating lymphocytes observed in the tumor microenvironment, suggesting multiple favorable biologic effects of IL 12 expression Kaplan Meier Survival in GL261 Orthotopic Syngeneic Mouse Glioma Model Glioblastoma Multiforme: IL 12 Preclinical Activity Measuring Survival 13 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 0 10 20 30 40 50 60 70 80 0 20 40 60 80 100 DC no vector DC RTS IL12 (MOI 10000) Ad RTS IL12 (5x10 9 ) AL chow Ad RTS IL12 (5x10 9 ) + AL DC RTS IL12 (MOI 10000) + AL Time (Days) No Treatment Significant Market Potential for Ad RTS IL 12 14 Melanoma 76,690 Breast Cancer 234,580 Incidence Glioma 18,000 A Growing Oncology Portfolio 15 Compound Pre Clinical Phase 1 Phase 2 Ad RTS IL 12 IND Melanoma Breast GBM Cell based programs Immuno Oncology programs Cell signal targeting Multigenic platforms Human allogeneic mesenchymal stem cells genetically modified with genes that activate the immune system to destroy cancer Multigenic therapeutic antibodies such as single chain versions of Herceptin and Erbitux Embedded cellular bioreactors to deliver multiple proteins systemically using RheoSwitch platform DNA Combination Therapies: Potential Future INDs 16 * AACR NCI EORTC 2013 Upcoming Clinical Milestones 17 Program Milestone Timing Breast cancer Initiate Phase 2 combination study with SOC 1H 2014 Report preliminary data 1H 2015 Report results from ongoing Phase 2 study 2014 Melanoma Initiate Phase 2 combination study with SOC 1H 2014 Report preliminary data YE 2014 Report results from ongoing Phase 2 advanced melanoma study 2014 Glioblastoma Initiate Phase 1/2 dose escalation study 1H 2014 Report preliminary data YE 2014 Approx. 100 million shares outstanding Approx. $68 million in cash and investments No debt Development partner/top shareholder: 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, 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.

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.

March 2014 The Future of Cancer Therapy www.ziopharm.com 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. Forward looking statements are statements that are not historical facts.

Page 19 NASDAQ: ZIOP The Future of Cancer Therapy www.ziopharm.com