The phenotype and allele frequencies of alpha-1-antitrypsin has been studied by an IEF technique (pH 4.2–4.9) in ten population samples from the Balkans. The allele frequencies varied from 0.6667 to 0.7361 (*M1), 0.1100 to 0.1793 (*M2), 0.0992 to 0.1700 (*M3), 0 to 0.0105 (* S), 0 to 0.0078 (*Z) and 0 to 0.0172 (others). The results were compared with data from South and Middle European populations from the literature. Most of the populations form a cluster with small genetic distances, and a weak relationship to geographical distributions. In contrast, the samples from Southern France, the Iberian Peninsula and Madeira form a clearly separated cluster. The differences are mainly based on high frequencies of PI*S in the latter populations.