In order to investigate the contents of mycotoxins in commercial foods in Taiwan, a total of 356 samples from convenient stores, supermarkets and grocery stores located in 22 counties of Taiwan were collected from February to September, 2012. The samples were analyzed for aflatoxins, ochratoxin A, patulin, and citrinin by the methods promulgated by the Department of Health (DOH). Among them, 342 samples (96.1%) complied with the regulation set by DOH. Fourteen samples, including 2 peanut candy, 1 pistachio and 1 sichuan peppercorn were found contaminated with aflatoxins at levels above the maximum levels, 15 ppb for peanut, 10 ppb for nuts and spices, in Taiwan. Ten red yeast rice samples contained citrinin above 5 ppm, exceeding the maximum allowed level in Taiwan. The result of this survey has been sent to the local government in order to enforce the penalties to the suppliers of the violative samples.