We have analyzed the extent of genetic variation at nine autosomal short tandem repeat loci (D3S1358, vWA, FGA, THO1, TPOX, CSF1PO, D5S818, D13S317, D7S820) in six populations from Croatia, five of which are distributed in the islands of the eastern Adriatic coast and one is from the mainland. The purpose is to investigate the usefulness of these loci in detecting regional level genetic differentiation in the studied populations. Significant heterogeneity among the island and mainland populations is revealed in the distributions of allele frequencies ; however, the absoulute magnitude of the coefficient of gene differentiation is small but significant. The summary measures of genetic variation, viz., heterozygosity, number of alleles and allele size variance, do not indicate reduced genetic variation in the island populations compared to the mainland population. In contrast of the two measures of genetic variation, allele size variance and within locus heterozygosity, the imbalance index (b) indicates evidence of recent expansion of population sizes in all islands as well as in the mainland. High mutation rates of the studied loci, together with local drift effects are likely explanations for inter-island genetic variation and the observed lack of reduced genetic diversity among the island populations.