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To determine if human papillomavirus (HPV) in the primary tumor was associated with disease-free survival of stage Ib cervical cancer patients, archival tissues from 47 patients were analyzed for HPV DNA by in situ hybridization (ISH) and polymerase chain reaction. HPV integration was determined by ISH signal pattern. Laboratory data were correlated with clinical parameters and disease-free survival. Kaplan-Meier estimates of 4-year disease-free survival were 56% in women with HPV detected in the primary tumor by ISH and 100% for women in whom HPV was not detected (P = .02). Four-year disease-free survival was 39% for patients with integrated HPV in the primary tumor (P = .005 vs. HPV-negative tumors and .05 vs. HPV episomal or episomal/integrated). HPV detection and integration state was not associated with any other clinical variable. Detection of integrated HPV DNA in the primary tumor was strongly associated with treatment failure.