The effect of ochratoxin A (OTA), fumonisin B(1) (FB(1)), and their combinations on DNA damage was studied using the standard alkaline comet assay and the Fpg-modified comet assay. Rats were orally receiving OTA (5 ng/kg b.w., 0.05 mg/kg b.w., and 0.5mg/kg b.w., respectively) for 15 days, FB(1) (200 ng/kg b.w., 0.05 mg/kg b.w., and 0.5mg/kg b.w., respectively) for 5 days, and the combinations of two lower OTA and FB(1) doses. The tail length, tail intensity, and Olive tail moment (OTM) obtained with the standard comet assay and Fpg-modified comet assay were significantly higher in treated animals than in controls, even at the lowest dose of OTA or FB(1) (p<0.01). The Fpg-modified comet assay showed significantly greater tail length, tail intensity, and OTM in all treated animal than did the standard comet assay (p<0.05), which suggests that oxidative stress is likely to be responsible for DNA damage. DNA damage detected by the standard comet assay at all OTA or FB(1) doses indicates that some other mechanism is also involved. Combined OTA+FB(1) treatment measured either by the standard comet or the Fpg-modified comet assay showed a synergistic increase in the tail intensity and OTM in kidney cells, even at doses that correspond to the daily human exposure in Europe.