Vitamin D deficiency is an important public problem worldwide because of its link to many diseases and poor health outcomes. However, there is limited data on the vitamin D status of African populations. We aimed to determine the prevalence and risk factors associated with vitamin D deficiency in Africa. To achieve this, we searched for, reviewed and summarized all studies that measured the vitamin D status of populations living in Africa. We then pooled the vitamin D deficiency prevalence estimates from the individual studies to come up with an overall prevalence for vitamin D deficiency. On average, we found that about one in every three people in Africa had vitamin D deficiency, that is, had vitamin D levels below 50 nmol/L. Groups most at risk of vitamin D deficiency included newborns, women, urban residents and populations living in northern and southern Africa. This is of particular concern for Africa, because African populations have one of the highest reported cases of rickets in the world. In addition, Africa has a large burden of infectious disease, and the burden of non-communicable diseases is rising, diseases which have been linked to vitamin D deficiency. Health care providers, policy makers and the general public should be aware of the high prevalence of vitamin D deficiency in Africa and the associated health risks. We recommend that public health strategies in African countries should include efforts to improve the vitamin D status of African populations.