Y-chromosomal microsatellites (STRs) are potentially useful in forensic practice but, in contrast to autosomal systems, large and diverse population databases are required in order to facilitate the statistical evaluation of donor-stain matches. Since appropriate data from the Baltic region have so far been lacking, blood samples were obtained from 430 males originating from one of the three Baltic states and these samples were genotyped using a previously described "extended core set" of nine Y-STR marker systems. Allele frequency distributions and discrimination indices were calculated, and the three populations were tested for genetic differences by means of analysis of molecular variance (AMOVA). A larger genetic difference became apparent between Estonian and both Lithuanian and Latvian males than between the latter two, non-Finno-Ugric speaking populations. The haplotype data reported here have been included into the Y-STR database maintained at the Institute of Legal Medicine, Humboldt University, Berlin.