Systematic application of molecular techniques for epidemiology may serve as a useful tool in the evaluation of HIV transmission in small populations, and allows for better targeting of prevention programs while complementing classical epidemiological methods and preserving the privacy of individuals. Coded serum samples from 24 randomly chosen patients belonging to the HIV cohort of Berne were investigated by direct assessment of partial env gene sequences. This information was used to construct a preliminary sequence database. Thereafter, nine couples, amongst whom HIV transmission was thought possible, were assessed in a blind and coded fashion. Sequence data demonstrated that the main viral subtype circulating in Berne has the characteristics of the American-European HIV-1 strain (96% amino acid homology). 4 of 9 couples were shown to share viral strains. Other potential couples carried strains with sequence characteristics that did not support the possibility of transmission. These data provide a basis for future epidemiological studies in our community.