Services that aim to prevent mother-to-child HIV transmission (PMTCT) can simultaneously reduce the overall impact of HIV infection in a population while also improving maternal and child health outcomes. By taking a health equity perspective, this retrospective case control study aimed to compare the health status of under-5 children born to HIV-positive and HIV-negative mothers in Tigray Region, Ethiopia. Two hundred and thirteen HIV-positive women (cases), and 214 HIV-negative women (controls) participated through interviews regarding their oldest children. Of the children born to HIV-positive mothers, 24% had not been tested, and 17% of those who had been tested were HIV-positive themselves. Only 29% of the HIV-positive children were linked to an ART programme. Unexpectedly, exposed HIV-negative children had fewer reports of perceived poor health as compared to unexposed children. Over 90% of all the children, regardless of maternal HIV status, were breastfed and up-to-date with the recommended immunizations. The high rate of HIV infection among the babies of HIV-positive women along with their low rates of antiretroviral treatment raises serious concerns about the quality of outreach to pregnant women in Tigray Region, and of the follow-up for children who have been exposed to HIV via their mothers.