Birth defects (BDs) are functional and structural alterations in embryonic or fetal development. With an incidence of approximately 3-5%, BDs are a leading cause of infant mortality and lifelong disability. A population-based prospective case-control study was conducted for one year with 5204 infants, between March 1 st , 2011 and February 29 th , 2012 in the city of São José do Rio Preto, State of São Paulo, Brazil. The incidence of BDs was 3.2% [95% confidence interval (95%CI): 2.8-3.8%]. The most common congenital anomalies were heart diseases in isolation (11.2%; 95%CI: 7.3-16.9%) followed by Down syndrome (9.5%; 95%CI: 5.9-14.8%), neural tube defects (8.9%; 95%CI: 5.4-14.1), urinary tract anomalies (7.7%; 95%CI: 4.4-12.7%), and polydactyly (7.0%; 95%CI: 4.0-12.0%). The majority of mothers with Down syndrome babies had advanced age. Family members with the same BD, maternal alcohol consumption, gestational diabetes, and previous miscarriages were the most frequent risk factors. The results were similar to published data from other countries except for the incidence of Down syndrome, which was twice as high as reported by other authors and is probably due to the high sociocultural level of the region where the current study was performed, leading to pregnancies at older maternal age.