Deoxynivalenol (DON), zearalenone (ZEN), and fumonisin B₁ (FB₁), as the main mycotoxins contaminating rice, often coexist in food. Thus, we have measured the genotoxicity of the three rice fungal contaminants, singly and in different combinations, with a 28-day multi-endpoint (Pig-a assay + in vivo micronucleus [MN] test + comet assay) genotoxicity platform. Male Sprague–Dawley rats received the agents orally via gavage for 28 consecutive days, before performing the abovementioned tests. Results indicated that low dose of a single mycotoxin did not show significant genotoxicity. However, some of these mycotoxins in combination induced significant genotoxicity in the peripheral blood and tissues, at sacrifice. In the peripheral blood, the binary combination of DON and FB₁ significantly induced MN. In the liver, ZEN might aggravate the DNA-damaging effects of DON and FB₁. Therefore, the genotoxicity of sub-chronic exposure to mycotoxins in combination cannot be ignored.