From a posteriori analyses of genetic variation, recombination can only be identified when the parental genomes are distinct. For viruses like HIV-1, this requires the producer cell to be infected by more than one virus. Using fluorescence in situ hybridisation, the provirus copy numbers in splenocytes from two HIV-1 patients were determined. More than 75% of infected splenocytes harboured two or more proviruses, range 1-8, with a mean of approximately 3-4 per cell. Sequencing of amplified DNA from single laser micro-dissected cells showed an extraordinary degree of diversity while numerous recombinants were evident. Given the dynamics of HIV-1 turnover in vivo and a recombination rate of approximately 3 cross-overs per cycle, some genomes from a fifteen year old infection may have undergone as many cross-overs as bases in the genome. Thus, recombination profoundly influences HIV evolution and gives it a non-clonal and transitory nature in vivo.