A population study of Hungarian Romanies was carried out on the STR loci HumLPL, HumF13B, HumFES and HumF1301. There was little evidence for association of alleles within/between the four STR systems. Allele frequency distributions were significantly different between the Romany and the previously reported Central Hungarian population databases. Population differentiation was estimated by computing F- and phi-statistics as well as frequency estimate differences of individual phenotypes for these two population samples. The results suggest that the population structure may have an effect on the interpretation of forensic DNA evidence in Hungary. Phylogenetic tree reconstruction with six populations from three major ethnic groups revealed a relatively distant genetic relationship of the Baranya Romanies with other Caucasian populations.