The impact of parental ages and of various maternal characteristics having a possible effect on congenital anomalies is examined using linked national data sets on mothers, live births, and congenital anomalies for the Czech Republic and for the period 2000-2007. Logistic regression modelling shows that both maternal and paternal ages are associated with anomalies of cleft lip and cleft palate and anomalies of the musculoskeletal system.