To investigate the relationship between prepregnancy maternal body mass index (BMI) and congenital anomalies (CAs). Case-control study on data collected by the registry of CAs of Tuscany (Italy) and birth certificates from 2005 to 2017. Maternal prepregnancy BMI. Any major CAs and groups of organ-specific anomalies. Odds ratios (ORs) were estimated using logistic regression models adjusted for maternal factors. Maternal BMI ≥25 was significantly associated with all nervous system anomalies (OR=1.61, 95% confidence interval [95% CI] 1.13-2.29) and with neural tube defects (OR=2.03, 95% CI 1.00-4.12); maternal underweight was significantly associated with orofacial clefts (OR=1.67, 95% CI 1.12-2.48). After stratification by education, in the low education group, mothers with BMI ≥25 had an increased risk of nervous system anomalies (OR=2.19, 95% CI 1.01-4.76), whereas underweight mothers had an increased risk of nervous system anomalies (OR=3.89, 95% CI 1.44-10.53), orofacial clefts (OR=2.59, 95% CI 1.24-5.42), and urinary anomalies (OR=1.74, 95% CI 1.07-2.82). In the medium/high education group, the only significantly increased risk was found in mothers with BMI ≥25 for nervous system anomalies (OR=1.50, 95% CI 1.00-2.25). Main results have shown a positive association of maternal BMI ≥25 with nervous system anomalies and maternal underweight with orofacial clefts. The study has also evidenced the impact of social status and provided clues to the role of maternal ethnic background.