Background: Over the years, poor medical documentation is a well known phenomenon in medical practice but the magnitude of the problem in our setting has not been defined.Objective: To assess the overall frequency of missed detection of anomalies of external genitalia following the routine newborn physical examination and to describe the general pattern of its documentation.Methods: In this hospital-based descriptive cross-sectional study, 915 full-term newborn infants in an open population survey were systematically screened for anomalies of the external genitalia, using a checklist derived by modifying parameters in the Prader scoring system and the External masculinization score charts. The pattern of documentation was assessed in 915 case files. The findings of the researchers were then compared to those previously documented by the attending physician/midwife. The study was conducted in two Nigerian hospitals (University of Benin Teaching Hospital and St Philomena Catholic Hospital) in Benin City. All members of staff of the two hospitals were blinded to the fact that the previous examination findings documented in the case files were being assessed during this study.Results: Of the 915 infants, 19 (2.1%; 95% CI= 1.2-3.0) had anomaly of the external genitalia at birth. The overall frequency of missed diagnosis of external genital anomalies was 68.4% with undescended testes (UDT) being the most frequently missed. The level of documentation of the findings of the external genital examination was poor in both hospitals. Combining the two hospitals, the external genital examination findings were not documented in 76.1% of case files.Conclusions: The routine newborn examination as currently practiced in the two hospitals was weak in detecting external genital anomalies. Poor documentation of the external genital findings is a common occurrence in the setting where we practice, irrespective of whether the health institution is tertiary or secondary.Key words: Audit, clinical documentation, external genitalia anomalies, missed diagnosis, routine newborn examination.