ABSTRACT This is a prospective observational study on the profile of central nervous system (CNS) anomalies in a neurosurgical unit in Ikeja, Nigeria. All cases of CNS anomalies seen by the authors in 1 year, January to December 2005, were analyzed. Descriptive variables include some demographics of the patients and their parents; profiles of CNS anomalies, cranial or spinal, neural tube defects (NTD) or others; presence of associated anomalies; and rate of surgical correction of these anomalies. Sixty‐one cases were recorded, approximately 64% of our total pediatric neurosurgical output. Forty‐one cases were males, 20 females, with a male to female ratio of approximately 2 to 1. The age at presentation ranged from 2 days to 60 months (mean 5.6 months) and the majority of the parents were young (the mean ages of the fathers and mothers were 35 years and 28 years, respectively), and low income earners (70%). The cases comprised cranial (61%) and spinal (39%) anomalies, or 54% of NTD versus others. The cranial lesions were mainly congenital primary hydrocephalus in 44% of cases, encephalocele in 28%, and microcephaly in 17%. The spinal lesions were spinal dysraphism in more than 90%; all in the lumbosacral region. Seventy percent of the NTD had associated cranial or other system anomalies, mainly secondary hydrocephalus in 65%. The surgical correction rate of all of these cases was 38%. NTD were significantly more likely to present early, be associated with other anomalies and undergo surgical correction in this series (P < 0.001). CNS congenital anomalies are under‐reported in Nigeria and other developing countries. A call is made for the establishment of nationwide efforts to fully clarify the epidemiology of this silent epidemic.