To determine the prevalence of major congenital heart defects (CHD) by ethnicity and sex.Data from the Florida Birth Defects Registry was used to conduct a retrospective cohort study with 8029 singleton infants with 11 CHDs born 1998–2003 to resident non-Hispanic (NH) white, NH-black, and Hispanic women aged 15 to 49. Defect-specific prevalence rates, ratios, and 95% confidence intervals were calculated. Poisson regression was used to calculate adjusted ethnic-specific rate ratios (RR) for each CHD. Statistical significance was P < .0001.Compared with NH-whites, NH-black males had significantly increased rates of pulmonary valve atresia/stenosis (RR = 1.66) but lower prevalence of aortic valve atresia/stenosis (RR = 0.33) and ventricular septal defect (VSD; RR = 0.78). Hispanic males had lower rates of aortic valve atresia/stenosis (RR = 0.28), coarctation of the aorta (RR = 0.61) and VSD (RR = 0.79). NH-black females had statistically significantly lower rates of VSD (RR = 0.75), and Hispanic females had lower rates of tetralogy of Fallot (RR = 0.54), VSD (RR = 0.84) and atrioventricular septal defects (RR = 0.53) compared with NH-whites.We found differences in ethnic susceptibilities to CHD by sex, but the cause remains unclear.