Background: Nevirapine prophylaxis has been found to lower the risk of HIV transmission in breast-fed infants. While about 95% of pregnant and lactating mothers use Antiretroviral therapy in Uganda, a smaller percentage of HIV exposed infants (HEI)receive nevirapine (NVP)prophylaxis. This study aimed to determine the proportion of HEI whomissed NVP prophylaxis and associated factors. Methods: This was a cross-sectional study done using quantitative methods. It was conducted at Mulago National Referral Hospital. A total of 228mother-infant pairs were enrolled.The proportion of HEI who missed NVP, maternal, infant and health facility factors associated were measured using a pre-tested questionnaire. Bivariate analysis and binary logistic regression model were used to determine the proportion and factors associated with missing NVP prophylaxis. Results: The proportion of HEI who missed NVP prophylaxis was 50/228(21.9%). Factors significantly associated with HEI missing NVP prophylaxis included; delivery from outside government health facilities [AOR=8.41 95% (CI 3.22-21.99)], mothers; not undergoing PMTCT counselling [AOR=12.01 95% (CI 4.53-31.87)],not on ART[AOR=8.47 95% (CI 2.06-34.88)] and not having disclosed their HIV status to their partners [AOR=2.80 95% (CI 1.13-6.95)].The HEI that missed nevirapine and were HIV positive were 35 (70.0%). Conclusion: One in five HEI missed NVP prophylaxis and nearly three quarters of those who missed NVP prophylaxis were HIV infected. Improving uptake of nevirapine by HEI will require interventions tostrengthen PMTCT counselling, assisted partner notification, reduction of HIV stigma and support to the private sector in the provision of PMTCT services.