We describe a rare case of refractory lower urinary tract symptoms in a young woman caused by human papillomavirus (HPV) infection. Concurrently, vulvar and vaginal warts were present, particularly near the external urethral meatus. Biopsy of the whitish plaque in the trigone of the bladder demonstrated signs of HPV infection and bladder leukoplakia; polymerase chain reaction analysis of this tissue was positive for HPV16. Systemic and local treatments for HPV infection were prescribed. All symptoms resolved. Follow-up examination revealed negative HPV DNA in the bladder tissue.