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Objectives To assess the prevalence and patterns of externally visible structural birth defects in the Tigray Region during the war and siege period.Design Retrospective hospital-based cross-sectional analysis of delivery records from 11 public hospitals in the Tigray Region of Ethiopia.Setting 11 selected public hospitals that remained relatively functional during the war in the Tigray Region of northern Ethiopia and provided maternity and neonatal care.Participants All recorded delivery outcomes between October 2020 and December 2023 were reviewed. A total of 54 626 birth records, including both live births and stillbirths, were analysed. Each record was systematically screened to identify the presence and type of birth defects.Primary and secondary outcome measures The prevalence and patterns of externally visible structural birth defects were evaluated using retrospective hospital delivery record reviews. The primary outcome was the prevalence of externally visible structural birth defects per 10 000 births. Secondary outcomes was the distribution of the specific types of the congenital anomalies, the proportion of stillbirth among affected births and characteristics related to maternal antenatal care (ANC) and folate supplementation.Results Among 54 626 deliveries reviewed, 2055 cases (3.8%) involved externally visible structural birth defects, corresponding to a prevalence of 376.2 per 10 000 births (95% CI 360.1 to 392.8). The most frequent anomalies were neural tube defects, particularly anencephaly (136.6 per 10 000 births) and spina bifida (110.6 per 10 000 births), together accounting for more than three-quarters of all defects. Other relatively common defects included hydrocephalus (33 per 10 000 births), clubfoot (23.4 per 10 000 births) and cleft lip/palate (20.5 per 10 000 births). A large proportion of affected births were stillbirths (73%). 82% of these mothers had not received periconceptional folate or multivitamin supplementation, and 87% did not attend ANC in the first trimester.Conclusion This study highlights a substantial burden of structural birth defects in the conflict-affected Tigray Region, Ethiopia. The findings underscore the urgent need to improve access to ANC and periconceptional folate supplementation. Future research should explore the role of environmental, nutritional and genetic factors in the observed rise in congenital anomalies.