Introduction: Birth defects are morphologic alterations diagnosed pre-, natal or postnatally. Surveillance systems have been used to estimate the prevalence in high complexity care centers; however, the variation of the prevalence among different complexity care centers remains unknown.Objective: To compare the prevalence of birth defects among two different complexity care centers in Cali, Colombia.Materials and methods: A descriptive hospital-based study following the methodology of the Latin American Collaborative Study of Congenital Malformations was conducted during 20 months in a medium complexity hospital and a high complexity hospital.Results: During the study period, 7,140 births were attended of which 225 had at least one birth defect. The prevalence of these was of 1.7% (IC95% 1.3-2.0) and 7.4% (IC95% 6.2-8.7) for the medium complexity hospital and the high complexity hospital, respectively. The highest frequencies for the high complexity care center were: ventricular septal defect, 10%; congenital hydronephrosis, 7%; abdominal wall defects, 6%, and hydrocephalus, 5%, while for the medium complexity were: polydactyly, 15%; preauricular skin tags, 8%; congenital talipes equino varus, 7%, and hemangioma, 6%.Conclusions: The prevalence of birth defects among different complexity care centers varies in quantity, type and severity of the anomaly diagnosed. The surveillance of birth defects is a useful tool for any level of care. It allows estimating more accurately the prevalence of the city, as well as being a base for the planning and targeting of resources according to the prevalence of different congenital defects.