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Ochratoxin A (OTA) and citrinin (CIT) are nephrotoxic mycotoxins produced mainly by fungal species Aspergillus ochraceus and Penicillium citrinum, respectively, which have been found to occur together in various food and feed commodities. In the present study, both OTA and CIT were evaluated for their potential to induce oxidative damage by determining lipid peroxidation (LPO) through malondialdehyde (MDA) assay and apoptosis by flow cytometry, gel electrophoresis and renal ultrastructural morphology in rabbits fed with diets containing OTA (0.75 mg/kg feed), CIT (15 mg/kg feed) and OTA + CIT (0.75 and 15 mg/kg feed, respectively) up to 60 days. The concentration of MDA was found significantly higher in OTA and combination-treated groups. OTA and combination-treated groups revealed more apoptotic cells in flow cytometry when compared with the CIT-treated group. Characteristic DNA fragmentation, as evidenced by ladder pattern in electrophoresis appeared in the toxin-treated groups. Ultrastructurally, interstitial cells showed nuclear fragmentation and cytoplasmic blebbing in OTA- and CIT-treated groups; whereas, proximal convoluted tubular epithelial cells, besides interstitial cells, showed nuclear fragmentation in the combined treatment group. The results suggested that low concentrations of OTA and CIT either alone or in combination induced apoptosis in a time-dependent manner and LPO in the rabbit kidney, which appeared to play a major role in the pathogenesis of nephrotoxicity. Furthermore, the interaction of these two nephrotoxic mycotoxins was found to be additive.