A retrospective study was conducted on the prevalence of congenital malformations in Cross River and Akwa Ibom states of Nigeria from 1980-2003. These states lie in the South-South geopolitical zone of Nigeria. The aim of the study was to determine the percentage of occurrence of birth defects and provide reference data for this part of the country. Details of congenital malformations were compiled by reviewing the delivery register of the records departments of maternity sections of University of Calabar Teaching Hospital, St Luke's Hospital Anua and St Mary's Hospital Uruakpan. A total of 127,929 births were recorded, of which 452 cases of malformations were recorded. The anomalies recorded in the skeletal system were the highest with 132 cases (29.2%) detected. Other malformations were found to be associated with the central nervous system with 111 cases (24.6%) detected. Those associated with the urogenital system were found in 83 cases (18.4%). Congenital anomalies of the lip, palate and jaw were found in 56 cases (12.4%), while those of the eye and ear were found in 12 cases (2.7%). Those of the gastrointestinal tract were found in 29 cases (6.4%), while those of the respiratory and cardiovascular systems were found in 28 cases (6.2%) and in one case (0.2%), respectively. Fifteen cases (3.3%) were associated with chromosomal abnormalities, such as Down syndrome. However, these results do not provide a complete incidence of congenital malformations in the two states studies because most anomalies are not recorded in rural health and traditional birth centers.