The effects of soil inoculation with A. flavus, variety and cropping system on the level of aflatoxin in stored maize were investigated under crop storage conditions in Benin. The experiment was organized in a factorial scheme (two varieties x two cropping system x with or without A. flavus soil inoculation) with eight treatments carried out in a completely randomized block design with three replications. A. flavus incidence in the plots soil was assessed both before and after soil inoculation. The harvested maize was stored for four months and cobs were sampled in a monthly interval and analyzed for the determination of Fusarium spp. colonization, Penicillium spp. and A. flavus cfu levels, insect pests population size and aflatoxin content. Multi-factorial analysis of variance and linear regression analyses with dummy variables were used to compare treatments. The concentrations of aflatoxin B1 and B2 in the kernels tended to increase with time during storage. Variety and fungal inoculation were the main factors influencing the levels of aflatoxins in stored maize. The improved variety showed a higher number of A. flavus cfu and aflatoxin B1 and B2 levels as compared to the local variety. Intercropping with Vigna unguiculata decreased the aflatoxin concentration in the improved variety but not in the local variety. The local variety had higher levels of Penicillium spp. and lower levels of Fusarium spp. than the improved variety. The treatments had no effect on the populations of the most common storage insect pests, but their levels were positively correlated with aflatoxin content. Both the initial inoculum level and the variety effect on the water content of the kernels after harvest played a significant role in A. flavus infection.