Modified AOAC 991.31 and AOAC 2000.03 methods for the simultaneous determination of total aflatoxins (AFs), aflatoxin B1, and ochratoxin A (OTA) in processed cereal-based foods by RP-HPLC coupled with fluorescence detection were validated. A KOBRA (R) Cell derivatization system was used to analyze total AFs. One of the modifications was the extraction procedure of mycotoxins. Both AFs and OTA were extracted with methanol water (75 + 25, v/v) and purified with an immunoaffinity column before HPLC analysis. The modified methods were validated by measuring the specificity, selectivity, linearity, sensitivity, accuracy, repeatability, reproducibility, recovery, LOD, and LOQ parameters. The validated methods were successfully applied for the simultaneous determination of mycotoxins in 81 processed cereal-based foods purchased in Turkey. These rapid, sensitive, simple, and validated methods are suitable for the simultaneous determination of AFs and OTA in the processed cereal-based foods.