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Introduction: the HIV-free survival rate is the gold-standard measure of the effectiveness of interventions towards prevention of mother-to-child transmission of HIV in any setting. However, data on HIV-free survival among the HIV-exposed infants followed up in most low-resource settings are lacking. We determined the HIV-free survival among breastfed infants in two tertiary facilities in a resource-poor setting in northern Uganda., Methods: we conducted a retrospective cohort study in May 2019 and retrospectively reviewed records of HIV-exposed infants registered in 2014 through 2016 at two tertiary facilities in northern Uganda. We analyzed data using SPSS v16 software package. The chi-square and Student t-tests were used to compare factors among infant groups. Multivariate logistic regression analysis was used to determine factors independently associated with HIV-free survival. P-value <0.05 was considered for statistical significance., Results: majority of the infants were males 55.6% (203/365) and 98.6% (360/365) received nevirapine prophylaxis. A total of 345 (94.5%) infants were exclusively breastfed, only 100/345 (29.0%) of whom were exclusively breastfed for at least 6 months, while the breastfeeding status of 44/345 (12.8 %) infants could not be ascertained. The overall HIV-free survival rate was 93.7% (342/365), while 2.7% (10/365) were HIV-infected and 3.6% (13/365) died. Infants´ age at enrolment in care (aOR 5.20, p=0.008) and treatment facility (aOR 3.76, p=0.027) were the independent determinants of HIV-free survival., Conclusion: the HIV-free survival rate among the breastfed infants in the study setting marginally falls short of the recommended standard, thus calling for more efforts to improve survival., Competing Interests: The authors declare no competing interests., (Copyright: Irene Aguti et al.)