To determine the variability of BK virus (BKV)in vivo, the sequences of nine full-length molecular clones from the striated muscle and heart DNA of a patient with BKV-associated capillary leak syndrome (BKVCAP), as well as three clones each from the urine of one human immunodeficiency virus type 2-positive (BKVHI) and one healthy control subject (BKVHC), were analysed. The regulatory region of all clones corresponded to the archetypal regulatory region usually found in urine isolates. Analysis of the predicted conformation of BKVCAP proteins did not suggest any structural differences on the surface of the viral particles compared with BKVHI and BKVHC clones. No amino acid changes common to most BKVCAP clones could be identified that have not already been reported in non-vasculotropic strains. However, the coding region of each clone had unique nucleotide substitutions, and intra-host variability was greater among BKVCAP clones, with a mean difference of 0·29 % per site compared with 0·16 % for BKVHI and 0·14 % for BKVHC. The clones from each strain formed monophyletic clades, suggesting a single source of infection for each subject. The most divergent BKVCAP clones differed at 0·55 % of sites, implying a rate of nucleotide substitution of approximately 5×10−5 substitutions per site per year, which is two orders of magnitude faster than estimated for the other human polyomavirus, JC virus.