Background: An estimated 1.2 percent of pregnant women are living with HIV in Ethiopia and sadly, one of every 3 children born to these women is infected with HIV. Elimination of these mother-to-child transmissions (MTCT) of HIV is possible through HIV testing during pregnancy and taking antiretroviral medications. However, only 24 percent of pregnant women living with HIV have yet received the medication needed to prevent MTCT of HIV in Amhara region, Ethiopia. Hence, there exists a concern that the rate of HIV infection among infants born to HIV positive mothers might be high. This study assessed the prevalence of HIV infection and associated factors among infants born to women living with HIV. Methods: All eligible records of HIV-exposed infants enrolled between January and December 2012 were reviewed from 17 health facilities which were providing PMTCT services. The study included 434 HIV-exposed infants having HIV DNA/PCR test result. Data were collected using structured data extraction formats. Data were then entered into EPI INFO Version 3.5.1 and analyzed by SPSS Version 16.0. Both bivariate and multivariate analyses were carried out to calculate odds ratios and to control for the effect of confounding. Result: The prevalence of HIV among exposed infants was 10.1%. Delay in HIV diagnosis (AOR = 1.3), mixed infant feeding (AOR = 8.8), failure to receive antiretroviral therapy during pregnancy or breast feeding (AOR = 21.6), failure to attend skilled delivery service (AOR = 6.1) and shorter duration of HIV treatment (AOR = 12) were the factors that increase the risk of mother-to-child transmission of HIV in this study. Conclusion: The prevalence of HIV among infants born to HIV positive women in the region is close to the national estimate of 10.9%. Delayed HIV diagnosis, inadequate use of antiretroviral therapy and lack of skilled delivery care were the factors that enhance mother-to-child transmission of HIV. Having such a significant figure in the era of the world’s pledge to eliminate MTCT of HIV is unbearable. Ensuring access and use of integrated PMTCT services should be the top priorities of the national PMTCT program.