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A simple and inexpensive single‐nucleotide polymorphism (SNP) analysis procedure is described that uses the Fotodyne Analyst System equipped with the Gel‐Pro Analysis software to compare the relative fluorescent intensity of ethidium bromide stained and MboI restricted amplicons from male individuals. The different intensity ratios reflect the ratio of repetitive elements with and without an MboI restriction enzyme site. The polymerase chain reaction (PCR) products represent a reiterated sequence within the Y‐linked deleted in azoospermia (DAZ) complex involved in male fertility in humans. This procedure was utilized to determine the ratio of MboI+ and MboI– repetitive sequences in 32 male individuals from two human populations, the Buryat from Mongolia and the Mayan from Yucatan. The proportion of wildtype to mutant amplicons was found to vary from 0 to 100% among individuals. This technique is well suited for large‐scale analysis of the locus investigated in this manuscript and other similar polymorphisms. This approach may contribute to the study of recent human evolution based on Y‐chromosome analysis as well as medical and developmental issues concerning the significance of these repetitive elements in male infertility.