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Mother-to-child transmission of HIV remains the most common source of paediatric HIV infection, accounting for 95% of cases, of whom, 90% are in sub-Saharan Africa. The purpose of the study was to explore the factors contributing to low retention rates of mother – Baby pairs accessing mother-baby care services at Rugazi HC IV.This study was retrospective and quantitative in nature. Data was collected by interviewing the study units, using the prepared and pretested questionnaire with 38 mother baby pairs participating in the study. Data was analyzed using Microsoft Excel spread sheet,tables, pie charts and bar graphs.The results showedthat the majority 81.6% had their spouses fail to escort them to the health facility and 57.9% self-transferred to other facilities. 84.2% respondents revealed that they were not followed up after missing appointments while 50% of mothers said that they were discriminated by community members. In conclusion, mothers in the study area were transferring themselves to other facilities, discrepancy in knowledge and fragmentation of service points within the health facility were the most leading factors the contributed to low retention of MBPs.Health service providers should be provided with knowledge on implications of retention of mother baby pairs, provision of support supervision to health units and improvement