Urine cytology was studied prospectively for the presence of human polyomavirus (HPV) in 17 consecutive patients undergoing marrow transplantation and correlated with hematuria and hemorrhagic cystitis. Of the 15 evaluable patients, nine had cytologic findings consistent with HPV infection during the first month after transplantation. Of these nine patients, two had gross and seven had microscopic hematuria, all without symptoms of cystitis. Hematuria resolved within 30 days of onset, although three patients had persistent cytologic evidence of HPV until 100 days after transplantation. During the follow-up ranging from 8 to 14 months, none of the patients developed hemorrhagic cystitis. Our data do not support the relationship between HPV and prolonged or severe hemorrhagic cystitis previously suggested by others, nor did we see any late onset hemorrhagic cystitis.