In a nested case–control study, we identified women who were successfully treated for CIN 3. Cases had biopsy proven recurrence, whilst controls remained disease free for at least five years. One hundred and seventy-two women were β-globin positive at diagnostic biopsy and at six-month post-treatment smear (90 controls and 82 cases). Thirty-nine cases (47.6%) were HPV16/18 positive at biopsy or follow up smear and 14 (17.1%) of 82 were positive at both. Of the controls, 37 (41.1%) were HPV positive at biopsy or smear with 3 (3.3%) positive at both. The unadjusted OR associated with being HPV positive at both points compared to being HPV negative at both was 8.0 (95% CI 2.13–30.37). The persistence of HPV 16/18 infection following the confirmed eradication of CIN is a highly significant risk factor for recurrence.