BackgroundIn 2014, there were 170,000 new HIV-infected children globally. The rate of HIV transmission from mother to child in Ethiopia was 18%. Though there are a number of HIV-related studies conducted in Ethiopia, there is a scarcity of evidence on the rate of mother to child transmission. So, the aim of this study was to determine the rate of HIV transmission and associated factors among HIV-exposed infants in selected health facilities in East and West Gojjam Zones, Northwest Ethiopia.MethodsRetrospective cohort study design was conducted. A total of 305 exposed infant- and mother pairs were included in this study. Data were collected from seven selected health facilities in East and West Gojjam Zone, Northwest Ethiopia. The study included a four-year duration PMTCT data, registered from July/2011 to July/2015. Data was collected using a prepared checklist. Data was entered using EpiData and analyzed using SPSS software. Descriptive, bivariate and multiple variable logistic regression analysis were conducted. A p-value less than 0.05 were used to declare statistical significant association.ResultThree hundred five infants and their mothers were included in this study. The mean age of mothers was 27.4 with a standard deviation of 4.3 years. The majority, 96.4% of infants were on exclusive breastfeeding before six months. The rate of HIV transmission at the end of 24 months were 5.9% (95% CI: 3.9%–7.9%). The number of positive children was reduced from 14 (10.29%) to 4(2.37%) due to the program shift from option A to option B+. Factors which were associated with transmission of HIV from mother to child were; children who were born from older mothers (AOR = 5.4, 95% CI = 1.15, 25.70), and infants whose mother couldn’t get PMTCT intervention (AOR = 15.95, 95% CI = 3.35, 75), and mothers who became pregnant after they knew they were HIV positive (AOR = 0.22, 95%CI = 0.049,096).ConclusionsThere is significant progress on the reduction of the rate of HIV transmission from mother to child in Ethiopia. Age of the mother, status of the mother at an entry to PMTCT program and presence of PMTCT interventions were significant factors associated with HIV transmission. Hence, the above factors should be given due emphasis on controlling HIV transmission from mother to child.