The goal of our study is to describe the prevalence of congenital anomalies (CA) in hospitals of the City of Buenos Aires, Argentina, according to two proxy variables of the socioeconomic level: health subsector, public (PUB) versus private/social security (PRI), and geographical location, northern (N) versus southern (S). The source of data was the National Network of Congenital Anomalies of Argentina (RENAC) (period 2010-2016). From a total of 228,208 births, 4872 newborns with CA were detected (2.14%). The prevalence in PRI-N, PUB-N, PRI-S, and PUB-S hospitals were 1.59%, 1.91%, 2.20%, and 2.43%, respectively. Prevalence of neural tube defects, abdominal wall defects, and oral clefts was significantly higher in PUB than in PRI hospitals. Prevalence of critical heart defects was significantly lower in PUB-N and in PRI-S hospitals. Prevalence of anencephaly, encephalocele, hydrocephalus, microcephaly, gastroschisis, cleft lip and palate, ductus arteriosus, and bilateral renal agenesis was higher in PUB hospitals, both N and S, as well as microphthalmia/anophthalmia and ambiguous genitalia, spina bifida, anotia/microtia, postaxial polydactyly, and diaphragmatic hernia had higher prevalences in PUB-S hospitals. Omphalocele was more frequent in PUB-N hospitals. Results suggest that vulnerable populations in the public and southern subsectors of the city still require a greater support to reinforce resources and strategies that lead to greater equity in access to health.