Human cytomegalovirus (HCMV) strains can be classified into different glycoprotein B (gB) genotypes. In a previous study, frequent intragenic variation of the gB gene was shown. The aim of this study was to analyse whether gB variation was due to homologous recombination. The gB gene of DNA extracts derived from the peripheral blood leukocytes of 14 immunosuppressed patients was amplified by PCR and cloned. Three variable sites of gB were analysed by restriction fragment analysis and DNA sequencing and compared with published prototypic strains. In three patients doubly infected with two distinct HCMV gB strains, prototypic (60-85 %) and nonprototypic recombinant strains (5-40 %) were detected. To demonstrate that homologous recombination is driving HCMV gB variability, cells were coinfected with plaque-purified prototypic gB strains and recombinant gB genes were selectively amplified by PCR. gB recombinants were detected after 15 days of coculture and cross-over sites were determined by sequencing. These data indicate that homologous recombination contributes to the variability of the gB gene in vitro and in vivo.