Persistent human polyomavirus infection is asymptomatic with limited states of virus production in the healthy individual, in immunocompromised patients, however, infection may lead to uncontrolled virus growth and fatal disease. Predominantly the CNS and in rare cases the urogenital tract are affected. During the AIDS epidemic, the number of cases is steadily increasing, thus dictating the need for an early and fast differential diagnosis. Virological diagnosis is essentially based on the detection of virus products in tissue or body fluids. Although sensitive and specific diagnostic techniques are available for the diagnosis of polyomavirus infection, widely accepted standards are not yet reached. This is in part due to the low number of cases in the past, but also to asymptomatic viral activation in nondiseased patients. Thus, additional parameters have to be evaluated to provide complementary tools for differential diagnosis.