We have used a new method for binning minisatellite alleles (semi-automated allele aggregation) and report the extent of population diversity detectable by eleven minisatellite loci in 2689 individuals from 19 human populations distributed widely throughout the world. Whereas population relationships are consistent with those found in other studies, our estimate of genetic differentiation (Fst) between populations is less than 8%, which is lower than comparative estimates of between 10%–15% obtained by using other sources of polymorphism data. We infer that mutational processes are involved in reducing Fst estimates from minisatellite data because, first, the lowest Fst estimates are found at loci showing autocorrelated frequencies among alleles of similar size and, second, Fst declines with heterozygosity but by more than predicted assuming simple models of mutation. These conclusions are consistent with the view that minisatellites are subject to selective or mutational constraints in addition to those expected under simple stepwise mutation models.