In this study the risk factors that were associated with gross congenital abnormalities in the state of Penang were studied. The study constitutes various parts: a trend analysis, land use pattern and its association with congenital anomalies, qualitative, retrospective case control and a prospective cohort study. The participants for the case control and cohort study were recruited from the antenatal mothers residing in Penang. There was a high incidence of congenital anomalies among the Malay population although the majority of the population in Penang is Chinese. There was a cluster of cases among the fishermen in a village. Three groups of congenital anomalies were studied and they were hydrocephalus, Down’s syndrome, and cleft lip (CL) and cleft palate (CP). The risk factors identified were smoking, advanced age, low socio- economic status, diabetes, exposure to pesticides, and maternal and paternal occupational exposure to chemicals. Most of the cases were concentrated in the industrialized areas. The results that are presented here suggest that further attention needs to be focused on the possible association of exposure to chemicals and in-depth study on fishermen. The State of Penang is an industrialized state and a majority of them are manufacturing and electronic industries. There is an increased potential for hazardous exposure to chemicals if proper protection has not been carried out. Besides the higher incidence among the Malay population, a further in-depth study is needed to find the causes. In view of the public health concern, further studies and investigations with regards to the increased rate of incidence of congenital anomalies are justified to evaluate the role of exposure to chemicals and pesticides in relation to occupation; in addition, there needs to be a surveillance programme and a National registry for congenital anomalies in Malaysia.