ABSTRACT Introduction: Mother-to-child transmission (MTCT) of HIV accounts up to 9% of new infections. MTCT of HIV occurs during pregnancy, delivery or breastfeeding and it is the leading source of HIV infection among children below the age of fourteen. Despite the impact of the problem, data on the prevalence of mother to child HIV transmission and its predictors are limited in the study area. Therefore, the main objective of this study was to determine the prevalence of mother to child HIV transmission using polymerase chain reaction (PCR) based technique. Method: Across sectional study was conducted from 4th April to 31th July 2018 among HIV exposed children in health facilities of the Bahir Dar City administration. Blood Sample was collected using What man 903 A Dried Blood Sample (DBS) card from the child finger, toe or heel. Abbott m2000sp and Abbott m2000rt PCR machine was used for PCR molecular technique to determine the HIV status of the child. Structured questionnaire was used to generate demographic related data. Data was entered and analyzed using SPSS version 23. Descriptive statistics was used to present and summarized the findings. Results: 261 HIV exposed children and their HIV positive mothers were included in the study. Of the total enrolled mothers 210(80.5%) gave birth in the hospital, 192(73.6%) had spontaneous vaginal delivery, 139(53.3%) were at HIV/AIDS stage I and 10(3.8%) didn’t get prevention of mother to child HIV transmission (PMTCT) service. Out of the HIV exposed children 136(52.1%) were females, 72(27.6) had age less than six months, 65(25%) were underweight, 198(76%) served exclusive breast feeding before 6 months and 9(3.4%) didn’t get Antiretroviral (ARV) or infection prevention prophylaxis. The overall prevalence of mother to child HIV transmission was at 2.7% (7/261). Although it was not possible to test statistical significance of the potential predictors, due to our low positivity rate, all the 7(100%) HIV positive children were born by spontaneous vaginal delivery, 5 (71.4%) HIV positive children were born from mothers who had started ART during pregnancy or after delivery. Similarly, 6 (85.7%) HIV positive children were from mothers who had an elementary or high school education. Conclusions: This study showed otherwise a relatively low prevalence of mother to child HIV transmission among HIV exposed children. To explore the possible predictors, large-scale study with adequate sample size is warranted. Key words/phrases: MTCT, PCR, DBS, Maternal HIV infection