The number of children who have HIV continues to grow. Studies have confirmed dramatic survival benefits and mortality reduction for infants confirmed and managed as early as possible after diagnosis. With the advent of the Polymerase Chain Reaction technology, early infant diagnosis of HIV among children is easier and more reliable worldwide. Most HIV programmes in developing countries are donor dependent with less encouraging moves towards sustainability drive by the local health authority. The health systems also face a lot of challenges while implementing these programmes that would promptly identify HIV exposed babies as well as enrolment into care. This review examined challenges facing early infant diagnosis of HIV among infants in Nigeria.