Major congenital malformations are unrecognised as a major cause of neonatal morbidity in many African countries. We have studied the contribution of major congenital malformations to morbidity among neonates referred to the University College Hospital, Ibadan, Nigeria over a four year period (1992-1995). Major congenital malformations were found in 11.1% of 1276 neonatal referrals and ranked fourth among the most common problems in such neonates (after sepsis, jaundice and tetanus but ahead of prematurity and perinatal asphyxia). The commonest malformations seen included spina bifida (22.5%), anorectal malformation (13.4%), omphalocoele (9.9%) and tracheo-oesophageal fistula (8.5%). Neonates with major congenital malformations presented significantly earlier than other neonates but mortality during the first admission was similar in the two groups. It is concluded that major congenital malformations pose a significant burden of morbidity in referred neonates to the hospital. Health services planners should take this into account in order to allocate the necessary resources for the diagnosis and management of such children.