Human papillomaviruses play a pre-eminent role as the most frequent sexually transmitted virus in urology. However, a pathogenetic connection between these viruses and urological cancers has not been proved so far, in contrast to the correlation with cervical cancer. Our 10-year experience with urological partner diagnostics and therapy surveillance in 788 patients form the empirical basis for the detection of clinical and subclinical HPV efflorescences, rates of partner infection and the benefit of laboratory techniques for HPV detection. Commercial HPV test methods only detect a fraction of the HPV types affecting the external genitals and the urethra that are demonstrated in a reference laboratory. HPV analyses are not appropriate for routine diagnostics, but should be used solely in research projects.