Background: Congenital anomalies (CAs) are structural or functional abnormalities that occur during intrauterine life and can be identified prenatally, at birth or may be detected in infancy later. Aim: To compare the incidence and risk factors of neonatal congenital anomalies before and after war at Al-Thawrah Hospital, Sana'a, Yemen. Design: Retrospective cross-sectional study. Setting: The study was carried at Al-Thawrah Hospital – Sana'a, Yemen.Subjects:112 CAs cases before war and 170CAs cases after war. Tool: Structural questionnaire with three parts, demographic data, mothers' data and neonates' data. Results: The incidence rate of CAs were approximately doubled after the war, the risk difference was 20.32 per 10,000/year. There was no significant difference between mortality rates (P > .05). There was a significant difference between the birth weights. 87.1% of mothers were lived close to airstrike. Most of the mothers had neither chronic nor acute diseases. 60.1% of mothers have not used medication and 89.4% of mothers did not expose to radiation. Conclusion: The incidence rate of CAs was markedly high after the war. The common risk factors such as the nutritional status of mothers and exposure to medications and radiation after the war were seemed to be neutral. Recommendation: Establish a committee for investigation about the environmental pollution that may cause CAs during the war.