Background Partial urorectal septum malformation (pURSM) sequence (or ‘persistent cloaca’) is a rare congenital anomaly characterised by a confluence of the urethral, anal, and genital openings. This study describes the prevalence, additional anomalies, and pregnancy outcomes of pURSM sequence in England and Wales.

Methods All cases of pURSM sequence notified to seven congenital anomaly registers in England and Wales during 1985–2010, whether delivered as live births, spontaneous fetal deaths (≥20 weeks gestation), or elective terminations of pregnancy for fetal anomaly (any gestation), formed this population-based case series. Risks of spontaneous fetal and infant death were examined by the Kaplan-Meier method. Differences in prevalence over time, and between regions, were examined by multilevel Poisson regression.

Results 117 cases were recorded among 4,251,241 total births. 58 (50%) were delivered as live births, 6 (5%) as spontaneous fetal deaths, and 53 (45%) as elective terminations. The total prevalence was 2.8 (95% CI: 2.3–3.4) per 100,000 total births, increasing significantly over time (p = 0.002) and differing significantly between regions (p = 0.005). 77 cases (66%) had at least one additional major congenital anomaly outside the perineum, including 67 (57%) with renal, 29 (25%) with musculoskeletal, 26 (23%) with digestive system, and 24 (21%) with cardiovascular anomalies. The risks of spontaneous fetal and infant death were estimated as 8.9% (95% CI: 4.1–18.8) and 26.3% (95% CI: 15.1–43.4) respectively.

Conclusions This is the largest study of the epidemiology of pURSM sequence. This information should be valuable for families and health professionals whenever a case of pURSM sequence is diagnosed.