Congenital anomalies (CA) contribute to disabilities and health conditions throughout life. Furthermore, they can cause emotional distress to the mothers and children, who may also experience limitations in individual and social development. This study investigated the prevalence of CA and the relationship with maternal education and age according to local development in the extreme south of Brazil. This is a retrospective observational study with birth data from the Live Birth Information System from 2000 to 2017. The association between age and maternal education with the presence of CA was verified using multiple Poisson regression for robust variances in models adjusted for those variables with a preliminary significant association. A total of 5131 (1.5%) had some CA identified at birth between 2000 and 2017. Only advanced age (≥36 years) was associated with CA regardless of macro-region development (p ≤ 0.001). The highest risk was observed in regions with medium development (RR = 1.60; 95% CI 1.30–1.97). Maternal education (<8 years of study) was associated with CA only in mothers from macro-regions with very high development (RR = 1.27; 95% CI 1.03–1.54). These analyses confirmed that women of advanced age are at greater risk of having children with a CA regardless of maternal education and local development, but social characteristics can also have an influence, as regions with higher development had lower prevalence of CA
