This study aimed to evaluate the effect of fungicides on rice cultivation, regarding the occurrence and the distribution of mycotoxins in fractions of the processed grain, by a validated chromatographic method. A method based on extraction with acetonitrile:water, determination by HPLC-DAD, and confirmation by LC-MS was validated before the mycotoxin evaluation. Control samples and samples to which triazole fungicides had been applied were collected from experimental fields for four years. Results showed that 87% of the samples were contaminated with deoxynivalenol or zearalenone, and that all samples treated with fungicide were contaminated with some of these mycotoxins. Aflatoxin B(1) and ochratoxin A were found in 37% of the samples; half of them had been treated with fungicide. Therefore, fungicides tend to be stressors for toxigenic fungi found in the fields.