Abstract: Paddy and milled rice grown in Uganda were investigated during storage for natural contamination by various types of fungi and aflatoxins. Direct plating method using five isolation media including dichloran rose-bengal chloramphenicol agar (DRBC), dichloran 18 % glycerol agar (DG18), Aspergillus flavus/parasiticus agar (AFPA), pentachloronitrobenzene rose-bengal yeast extract sucrose agar (PRYES), and pentachloronitrobenzene potato sucrose agar media (PCNB-PSA) were used to determine the fungal contamination. Fungi were isolated and identified to species or genus level and percentage contamination level was calculated. During storage over a 270-day period between Nov.1998 and Aug. 1999, paddy rice recorded a total of 58 species belonging to 33 genera while the milled rice recorded 50 species belonging to 30 genera. The broadest spectrum of species on both types of rice were from the genera Fusarium, Aspergillus and Penicillium on all isolation media whereby, 11, 9, and 4 species respectively were recorded on the paddy, while 4, 10 and 4 species respectively, occurred on the milled rice. Eurotium was represented by 3 species; Cladosporium, Cochliobolus and Humicola were each represented by 2 species, while the remaining genera each had one species on the paddy rice. Eurotium was similarly represented by 3 species on the milled rice, Chaetomium, Cladosporium, Humicola, Paecilomyces and Scopulariopsis each had 2 species while the remaining genera each had only one species. Field fungi including Cochliobolus miyabeanus, Fusarium lateritium, F. stilboides, Khuskia oryzae, Pestalotiopsis guepinii, and Scytalidium lignicola were all predominantly isolated on the paddy rice grains but only during the first half of the storage period, declining thereafter except for S. lignicola. Storage fungi including Aspergillus candidus, A. flavus, Eurotium spp., Paecilomyces variotii, Penicillium spp. and Talaromyces spp. occurred sporadically. The majority of the paddy samples (60 %) screened for aflatoxins recorded contamination but none above 20 ppb, the maximum level allowed in foodstuffs internationally. Increase in moisture content of the paddy was recorded during storage, attaining a maximum of 12.9 %. The milled rice was however, comparatively less contaminated by fungi, and with both the field fungi and storage fungi recording relatively equal distribution. Milling (dehusking) removed most of the fungal propagules from these grains. Aflatoxin contamination was similarly scarcely recorded with 60 % of the milled samples not having indicated any contamination. Increase in moisture content occurred during storage, attaining a maximum of 13.98 %. Key words: Paddy rice, milled rice, field fungi, storage fungi, aflatoxins