The possible teratogenic effect of co-trimoxazole (sulfamethoxazole and trimethoprim, Bactrim [Roche], Septrin or Septra [Burroughs-Wellcome], Sumetrolim [EGIS]) was evaluated using the data set of the Hungarian Case-Control Surveillance of Congenital Anomalies. In the study period of 1980 through 1984, 1.25% of pregnant women who had healthy babies (negative control group) were treated with co-trimoxazole during pregnancy. In those who had babies with congenital anomalies the rate of co-trimoxazole use was 2.31%. The case-control analysis showed a significant increase of co-trimoxazole use only in the groups of cleft lip +/- cleft palate and hypospadias. However, drug use was not higher during the critical period in either of the congenital anomaly groups. The distribution of component congenital anomalies in 13 cases affected by multiple congenital anomalies did not show any characteristic pattern. Respiratory and urinary system diseases were mentioned significantly more frequently in pregnancies of index patients' mothers. This analysis did not indicate any teratogenicity of co-trimoxazole. The higher drug use can probably be explained by maternal disorders.