Monitoring in Ishikawa Prefecture (mean population; 1,150,000), during the 20-year period from 1981 to 2000, involved monitoring the prevalence of congenital anomalies starting at gestational week 22. The main objectives of the present study were (1) to investigate the trend over the past 20 years in the prevalence of congenital anomalies, and (2) to investigate whether there is area accumulation in congenital anomalies or not. In addition, the prevalence of well-known risk factors such as smoking, drinking and family history among cases with congenital anomalies was analyzed to obtain clues to the background of such anomalies. During the 20 years, more than 200,000 births have been observed. Thirty-three selected congenital anomalies, consisting mainly of external anomalies, were analyzed in this study. The percentage of children born with congenital anomalies did not change markedly between the first and second halves of the monitoring period, remaining at approximately 4.5/1,000 births. There was also no significant change in annual trends in either Ishikawa Prefecture as a whole or in the three regions within Ishikawa. The prevalence of congenital anomalies by type showed a significant decrease in anencephaly and spina bifida. In contrast, Down syndrome and microcephaly increased significantly. The mean maternal age for Down syndrome increased significantly from the first-half period to the second-half period. The percentage of children with polydactyly whose mother smoked were relatively higher than that for the other congenital anomalies.