Purpose To evaluate whether aleglitazar (Ale), a dual PPARa/gamma agonist, has additive effects on myocardial protection against ischemia-reperfusion injury. Methods Human cardiomyocytes (HCMs), cardiomyocytes from cardiac-specific PPAR gamma knockout (MCM-PPAR gamma(CKO)) or wild type (MCM-WT) mice were incubated with different concentrations of Ale, and subjected to simulated ischemia-reperfusion (SIR) or normoxic conditions (NSIR). Cell viability, apoptosis and caspase-3 activity were determined. HCMs were transfected with siRNA against PPAR alpha (siPPAR alpha) or PPAR gamma (siPPAR gamma) followed by incubation with Ale. PPAR alpha/gamma DNA binding capacity was measured. Cell viability, apoptosis and levels of P-AKT and P-eNOS were assessed. Infarct size following 30 min coronary artery occlusion and 24 h reperfusion were assessed in WT and db/db diabetic mice following 3-day pretreatment with vehicle, Ale or glimeperide. Results Ale (at concentrations of 150-600 nM) increased cell viability and reduced apoptosis in HCMs, MCM-WT and MCM-PPAR(CKO) exposed to SIR. In HCM, the protective effect was partially blocked by siPPAR alpha alone or siPPAR gamma alone, and completely blocked by siPPAR alpha+siPPAR gamma. Ale increased P-Akt/P-eNOS in HCMs. P-Akt or P-eNOS levels were decreased when PPAR alpha alone, PPAR gamma alone and especially when both were knocked down. Peritoneal GTTs revealed that db/db mice had developed impaired glucose tolerance and insulin sensitivity, which were normalized by Ale or glimepiride treatment. Ale, but not glimepiride, limited infarct size in both WT and diabetic mice after ischemia-reperfusion. Conclusions Ale protects against myocardial apoptosis caused by hypoxia-reoxygenation in vitro and reduces infarct size in vivo.