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BACKGROUND While it is widely known that maternal age at childbearing plays a role in the occurrence of Down syndrome, less is known about the effects of maternal age on other major congenital anomalies. Information on the possible effects of other maternal characteristics and of the age of the father is even scarcer. OBJECTIVE We present new results on the associations between parental ages and other maternal characteristics on the one hand, and congenital anomalies on the other, using linked data from three Czech registries on mothers, newborns, and malformations, for the period 2000-2007. METHODS As the variables are in a categorical format, binary logistic regression is used in order to investigate the relationship between the presence/absence of a congenital anomaly for each of the 11 types of anomalies considered, and for the set of predictors. RESULTS This research confirms that the age of the mother has an impact on the incidence of Down syndrome and other chromosomal anomalies. Paternal age is not associated with chromosomal anomalies, and, in this Czech population, has a rather slight effect on some of the congenital anomalies examined. Another finding of the present study is that various other maternal characteristics may affect the incidence of congenital malformations. CONCLUSIONS Based on a large dataset, this study concludes that the ages of both parents can be associated with congenital anomalies of the child, and that maternal characteristics other than age have also to be considered. COMMENTS Risk factors can be tentatively proposed if they are based on a plausible and suitably tested explanatory mechanism. Unfortunately, in the majority of individual cases of congenital anomaly, the cause of the condition is unknown, and is suspected to result from an interaction of multiple environmental and genetic factors. [ABSTRACT FROM AUTHOR]