Objectives: To estimate the incidence of genital warts in adolescents and analyze their relationship with the development of cervical squamous intraepithelial lesions (SIL). Study design: From 1993 to 2006 we followed 846 adolescents in the gynecology clinic of a public hospital in Rio de Janeiro. They were sexually active, had a normal smear test and no genital warts upon recruitment and completed two years of follow-up. Data were analyzed using EPI-INFO software. The research was approved by the hospital Ethics Committee. Results: The mean age at recruitment was 15.8 1.4 years and at first intercourse was 14.7 1.6. Sixtythree (7.4%) adolescents presented condylomata, 5.6% (48/846) during the first year of sexual activity and 1.8% (15/846) during the second year. Within two years, 20.5% (174/846) of the patients had an abnormal smear test. Seventy percent (44/63) of the patients with genital warts developed a SIL. The association between warts and SIL showed a RR = 4.2(3.3–5.3). Conclusions: The incidence of condylomatawas one third of the incidence of SIL and was higher during the first than in the second year of sexual activity. Adolescents with genital warts had a fourfold increase in risk of SIL and therefore should be carefully followed up.