In a study based on 173 individuals drawn from three endogamous, co-resident communities in the province of Punjab, the Awan, Khattar and Rajpoot, an analysis of 10 autosomal single tandem repeats on chromosomes 13 and 15 revealed distinctive genetic profiles in each community. A total of 99 different alleles were detected, with 28 alleles (28.3%) shared by all three communities. The mean private allele frequency was 7.7%. There was a reduction in heterozygosity and high average inbreeding effects (FIS and/or HS), particularly in the Awan, indicating genetic isolation and a high cumulative level of autozygosity. Genotyping with eight Y-chromosome STRs resulted in the construction of six haplotypes, one each for the Awan and the Khattar but four for the Rajpoot, suggesting marked variation in the patterns of male founder effects in the history of each community. The lower than expected levels of homozygosity observed at a number of loci may be indicative of cosegregation of the STRs with nearby early development genes subject to selection.