Background: Cleft deformities (lip and palate) have been reported to be the most commoncongenital craniofacial anomaly in several settings. In Uganda, though two previousstudies were conducted to determine the incidence of cleft lip and palate, the estimatesobtained from those studies may not be precise given the study settings. This study wasundertaken to establish the incidence of cleft deformities and provide data to plan forbetter management of these deformities. The Setting was the labour wards at MulagoNational Referral Hospital, Kampala Uganda. The main objective of this study was todetermine the incidence of cleft deformities (lip and palate) among neonates born betweenFebruary 2008 and February 2009Methods: Cross-sectional study of all neonates who were born in Mulago Hospital. Weexamined all new born children and determined the presence or absence of cleft lipand/palate. Socio-demographic data and risk factors such as smoking, alcoholconsumption, infections and exposure to drugs such as anti-convulsants and steroids werecollected.Results: Among twelve thousands seven hundred and thirteen neonates born in Mulagohospital between February 2008 and February 2009, seventeen neonates presented withcleft lip with or without cleft palate: this gives an incidence of 1.34 per 1000 newborns or134 in 100,000 newborns.Conclusion: The incidence of neonatal cleft deformities seems to lie between what waspreviously reported in 1961 and 1996 in Uganda.