© 2014 Elsevier Inc. All rights reserved. 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.