Genotypes for 53 short tandem repeat (STR) markers distributed at an average of 39 cM intervals throughout the genome were determined for 46 individuals from the village of Bengkala, Bali. This village of approximately 2200 individuals has an oral and written tradition suggesting genetic bottlenecks. The allele frequency distributions in Bengkala were compared with distributions obtained by typing individuals in the CEPH data base using a Kolmogorov-Smirnov two sample test. Twenty-eight of the 53 markers showed differences (P < 0.05) in distribution between the two populations. Allele frequencies of tetranucleotide STRs were much more similar between the two populations than were those of dinucleotide STRs (P < 0.043). Population heterogeneity in Bengkala was indicated by an excess of observed homozygosity, deviations from Hardy-Weinberg equilibrium at seven loci, and significant allelic associations between physically unlinked loci. In addition to providing information pertinent to the issue of genetic diversity of STRs in the human population, these analyses serve as a resource to map a gene causing non-syndromal autosomal recessive deafness in Bengkala, and to corroborate the anthropological study of the history and social structure of the village.