We evaluated microbial populations and aflatoxin production in unhulled and white rice from rice processing complexes of the National Agricultural Cooperative Federation in five regions in Korea and identified three predominant Aspergillus species. Fungal and bacterial populations in rice samples were significantly different between regions in 2007. Aflatoxins were also detected and varied at the levels of 2.45 - 3.43 ng per g unhulled rice grain and 1.29 - 2.09 ng per g white rice grain. Unhulled rice generally detected higher level of aflatoxins than white rice regardless of sampling regions; however, no significant differences were found in Anseong and Cheonan in 2005 and Cheonan and Gimpo in 2007. Aflatoxin production between sampling regions was not different regardless of rice type and sampling year. Although the fungal diversity was highly distinct from region to region, three Aspergillus isolates were predominant in the rice samples; thus, representative isolates AC317, AF57, and AF8 were selected and identified based on their morphological and molecular characteristics. Consequently, isolates AC317, AF57, and AF8 were identified as A. candidus, A. flavus, and A. fumigatus, respectively. These fungi can produce mycotoxins that are harmful for consumers and thus it is important to detect and reduce the population of storage fungi in rice.