OBJECTIVE: To estimate the incidence of congenital syphilis and identify its relationship with Family Health Strategy coverage. METHODS: An observational ecological study was carried out with both descriptive and analytical components, by two different approaches: one that explores a temporal series (2003 to 2008) and one that focuses on the 2008 data. The secondary data (epidemiological, demographic, and socioeconomic) were obtained from the Department of Informatics of the Unified Health System and the Brazilian Institute of Geography and Statistics. Analysis of the possible effects of the implementation of the Family Health Strategy on the prevention of congenital syphilis was performed on selected subgroups of counties according to two approaches: a) the variation of the average annual rate of incidence of congenital syphilis in different strata of Family Health Program coverage between 2003 and 2008 and the calculation of the simple linear regression coefficient; and b) a negative binomial regression analysis of data from 2008 to control for confounding factors. RESULTS: Increasingly trends of congenital syphilis notification in Brazil reflect social inequalities in the distribution of cases. The incidence of congenital syphilis was lower in the counties with high Family Health Strategy coverage; however, after controlling for the co-variables, such an effect might be attributed to the coverage of prenatal care and the demographic characteristics of the counties where the implementation of the Strategy was a priority. CONCLUSIONS: Despite the increase in prenatal care coverage, the actions implemented still exhibit low effectiveness in the prevention of congenital syphilis. Prenatal care performed by Family Health Strategy teams did not control syphilis better than the prenatal care performed within the context of other models of assistance.