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Cytology is a well recognized and utilized method for the detection of polyomavirus in urine specimens from renal transplant patients. The purpose of this 5 year 6 month retrospective study (January 1, 2003–June 30, 2008) was to report on the additional infectious agents detected in these specimens. Of the 7,116 urine samples from renal transplant patients that were processed for the detection of polyoma (BK) virus, 1,399 (19.7%) were positive for BK viral inclusions and 5,717 (80.3%) were negative. In addition, 347 specimens (4.8%) contained infectious agents including HPV (1.6%), Candida (3.2%), Herpes virocytes (0.03%), cytomegalovirus (CMV; 0.03%), and trichomonads (0.03%) either alone or in combination. Follow-up cervical, vaginal, and/or vulvar biopsies were available in six (5%) of the 115 specimens with cellular changes consistent with low-grade HPV infection: three showed high-grade squamous intraepithelial lesions, two showed low-grade squamous intraepithelial lesions, and one showed both types of lesions. Urinary cytology plays a role not only in the detection of BK virus but also other infectious agents, which have an impact on follow-up patient management. Diagn.