Grain collected from the top, middle, and bottom layers of each storage bag was analyzed to determine the number fungi on the kernel surface and the number of infected kernels. The number of fungi washed from the surface of the initial grain used for storage was 1.3 × 103 (SE = ± 302) CFU/g of maize. Fusarium and Penicillium were the major genera identified on the culture medium. After three months of storage, the most predominant fungi were Fusarium, Penicillium, and Aspergillus species. Alternaria species were also observed as well as other sporulating fungal colonies and yeast-like fungal colonies. In Indiana, 9.8 × 103 (SE = ± 637) CFU/g of maize was washed from the grain stored in the woven bags, compared to 3.7 × 103 (SE = ± 878) CFU/g of maize in the PICS bags. The number of fungi on the maize in the Arkansas PICS bags was not significantly different (P < 0.01) than the Indiana PICS bags (2.8 × 103 (SE = ± 481) CFU/g of maize). In contrast, grain in the woven bags in Arkansas had 3.0 × 105 (SE = 1.0 × 105) CFU/g of maize. Our analysis indicated no significant difference in the number of surface fungi between layers except in the woven bags stored in Arkansas (P < 0.01). In two of the replicate bags, the bottom layer had significantly (10-fold) more surface fungi than other layers, and in the third replicate bag, the middle had significantly more fungi than other layers. Overall there was no significant difference (P < 0.01) between replicates of each bag type for a given environment.