BK virus (BKV) and JC virus (JCV) are present within the renal system of most adults. Reactivation may be linked to immunodeficiency, since many of the extant virus strains have been isolated from urine or kidney tissue of patients who were receiving immunosuppressive therapy or who had disorders of the immune system. To more critically evaluate the relationship between immunodeficiency and viruria, urine samples from individuals infected with human immunodeficiency virus (HIV) with various degrees of immunodeficiency were screened for the presence of viral DNA. JCV viruria occurred in 24%-27% of immunocompetent control subjects and was not increased with immunodeficiency. By contrast, there were both qualitative and quantitative changes in BKV viruria in immunodeficient subjects. The incidence of BKV viruria was increased, and some immunodeficient subjects shed BKV at levels up to 3000 times greater than levels shed by any of the nonimmunodeficient controls. DNA sequence rearrangements in the viral regulatory region did not appear to be required for shedding of virus, although they were present in approximately 20% of samples.