The aim of this study was to determine the prevalence of and factors associated with cleft lip and palate in newborns in referral health facilities in the town of Bunia. The cross-sectional method, supported by documentary analysis, was used to carry out this study, which targeted all newborns registered in the referral health facilities in the town of Bunia. Percentage calculations were used to analyse the data. After analysing the data, this study revealed the following: - The prevalence of cleft lip and palate in the referral health facilities in the town of Bunia was 1.93%. - Cleft lip and palate were more common in male newborns (62.4%). 88.6% of newborns with cleft lip and palate were born in pregnancies of 37-42 weeks of amenorrhoea. Nearly half and more than 1/3 respectively of the mothers giving birth to babies with cleft lip and palate were in gestational age 2 and aged 18-24 years. - The mother’s history of alcoholism and diabetes were identified as factors associated with cleft lip and palate in newborns in Bunia. In the light of these results, it can be concluded that cleft lip and palate continue to be recorded in health facilities in Bunia and that innovative strategies should be used to raise awareness among women of childbearing age.