HIV-2 infection was diagnosed in two patients 15 and 24 years of age and, thereafter, in their mothers. Epidemiological data suggested that vertical transmission was the most probable mode of infection in both patients (Mota-Miranda A, et al.: AIDS 2001;15:2460-2461). Phylogenetic analysis of env C2-C3 sequences from the patients and their mothers was used in an attempt to confirm or exclude the events of perinatal HIV-2 transmission. Sequences from each putative transmission pair formed monophyletic clusters in phylogenetic analysis, a clear indication of common ancestry. Interpatient nucleotide distances increased with the period of infection being consistent with long-term infection. In conclusion, the results are consistent with an epidemiological linkage between the viruses infecting each mother-child pair and support the occurrence of perinatal HIV-2 infection in both cases. Application of similar phylogeny methods to other suspected transmission cases may permit a better understanding of the epidemiology and molecular evolution of HIV-2.