Objective: We evaluated time to clearance of high risk (HR) HPV infection in relation to functional variants in three genes ( CYP1A1, GSTT1, and GSTM1). Methods: The study group consisted of 450 HR-HPV infected women from the Atypical squamous cells of undetermined significance-low-grade squamous intraepithelial Lesion Triage Study (ALTS) cohort followed up at the clinical center at Birmingham, Alabama. The Cox proportional hazard model with the Wei-Lin-Weisfeld (WLW) approach was used, controlling for relevant covariates. Results: Women who were polymorphic for CYP1A1 experienced an HR-HPV clearance rate that was 20% (HR = 0.80, p = 0.04) lower than women without the polymorphism for CYP1A1, adjusting for all other cofactors. The GSTM1 null genotype was associated with higher HR-HPV clearance rate (HR = 1.39, p = 0.006). The polymorphism in GSTT1 was not significantly associated with time to clearance of HR-HPV. Conclusions: Xenobiotic metabolism genes may influence the natural history of HR-HPV infection and its progression to cervical cancer.