BackgroundCleft lip with or without cleft palate is one of the most common congenital anomalies that affect the oro-facial region. The aim of the study was to determine the period prevalence, pattern and perceptions of cleft lip and cleft palate in children born between 2005 and 2010 in two hospitals in Kisoro District, Uganda.MethodsThe study involved a retrospective review of medical records of mothers who delivered live babies between January 2005 and December 2010 in Kisoro Hospital and St. Francis Hospital, Mutolere in Kisoro District. Key informant interviews of mothers (n = 20) of the children with cleft lip and/or clip palate and selected medical staff (n = 24) of the two hospitals were carried out. The data were analysed using descriptive statistics.ResultsOver the 6 year period, 25,985 mothers delivered live babies in Kisoro Hospital (n = 13,199) and St. Francis Hospital, Mutolere (n = 12,786) with 20 babies having oro-facial clefts. The overall period prevalence of the clefts was 0.77/1,000 live births. Sixty percent (n = 12) of children had combined cleft lip and palate and the same proportion had clefts on the left side of the face. More boys were affected than girls: 13 versus 7. About 45% of mothers were hurt on realizing that they had delivered a child with an oro-facial cleft. Forty percent of mothers indicated that a child with oro-facial cleft was regarded as an outcast. About 91.7% (n = 22) of the medical staff reported that these children were not accepted in their communities. Surgical intervention and psychosocial support were the management modalities advocated for by most respondents.Conclusion/recommendationsThe period prevalence of combined cleft lip and palate in two hospitals in Kisoro District was comparable to some findings elsewhere. Cleft lip and cleft palate are a medical and psychosocial problem in Kisoro District that calls for sensitization and counseling of the families and communities of the affected children. The policy makers need to strategically plan for provision of rehabilitation with feeding obturators to facilitate easy feeding to gain weight before surgical intervention of the affected children.