Maize is one of the species with greater genetic diversity among cereals and possibly the most diverse crop species known. Accessing this variability is essential for maize breeding, allowing breeders to achieve progress of yield increasing, overcome environmental challenges or deal with pests and diseases. Among the maize diseases, southern rust is one of the most important, causing significant losses in yield and presenting severe epidemics worldwide. In the present study, the AFLP technique was applied to analyze population structure and genetic diversity among 145 tropical maize inbred lines, and to test for preliminary evidence of association between AFLP markers and the reaction to southern rust. Disease severity was evaluated in two crop seasons and the accessions were genotyped through AFLP using four primer combinations.