In this study, we analyzed the frequency, type and sex distribution of congenital anomalies of the central nervous system (CNS) at autopsy in the period prior to and after the Chernobyl accident in northwest Croatia, one of the areas with the highest exposure to nuclear contamination from Chernobyl. All autopsies in both periods were performed by the same technique, i.e. dissection of the trunk and head, and inspection of the extremities. There were 53 infants with congenital anomalies of the CNS in the period prior to, and 99 in the period after the Chernobyl accident. Our results showed a statistically significant increase in the incidence of CNS anomalies in general (chi 2 = 4,719, p < 0.05, D. F. = 1) and of neural tube defects (chi 2 = 5.380, p < 0.05, D. F. = 1) in the period after the Chernobyl accident. Differences in the incidence of various CNS anomalies, in all types of anomalies, and in sex distribution were not statistically significant. Studies of the association between the Chernobyl accident and congenital anomalies showed no clear changes in the prevalence of anomalies at birth which might have been associated with the accident. This study provided some additional data on the frequency of CNS anomalies in the period after the Chernobyl accident in one of the areas with the highest exposure to the nuclear contamination from Chernobyl. We suggest that the frequency of all anomalies, including CNS, in the period after the Chernobyl accident should be carefully monitored.