Abstract: Dramatic world economic changes have prompted most developing countries to reassess their varied educational programmes as well as the cost and benefit of such educational programmes. Most educationists have advocated the need to declare a state of emergency in our various educational systems which are not meeting the challenges of the 21st Century and neither helping to realize educational inclusion in the context of functional education lifelong learning, Education for all and realisation of the United Nations` Millennium Development goals. It is in the light of this development, that this study advocate the integration of the values of African Traditional Education System (ATES) and of Indigenous schools, embeded in Islamic and Quranic Schools into literacy learning and Nigeria`s educational system. Thus the paper reviews the concept, processes and facilities for indigenous education and schools in Africa. Discrepancies between school education system and the alternative systems are than outlined. How these could constitute a potentially cost-effective means of access to education to a larger clientele through the inculcation of basic skills, African values, apprenticeship scheme, functional, vocational education among others, that are relevant to the achievement of the Millennium Development Goals.