BACKGROUND seroepidemiological surveys suggest that approximately 20 % of women of childbearing age are susceptible to rubella. It is necessary to detect congenital rubella cases. Our objective was to determine the frequency of perinatal infection by rubella virus (RV) in infants with congenital heart disease. METHODS prospective, cross-sectional study. We studied hospitalized and outpatients from September 2007 to December 2008. Neonates and infants under one year of age with congenital heart disease were included. A blood sample of 3 mL was taken from mother-child binomial and micro-ELISA for IgG and IgM against rubella were performed. RESULTS 80 patients were studied, 56 % were female, with a median age of 3 months. More frequent congenital heart disease was ventricular septal defect (28.5 %), followed by atrial septal defect (17.5 %). Median maternal age was 28 years old. A history of febrile illness and rash during pregnancy was positive in 1.25 %. 7 cases of perinatal infection by RV were detected, three met the criteria for congenital rubella syndrome, and four had only congenital heart disease. CONCLUSIONS the search for cases of congenital rubella syndrome in newborns and infants with heart disease could be used as a strategy to detect non-obvious cases.