Africa is the continent with the highest density of regional organizations. Besides a continental/regional organization – the African Union – there are at least 18 sub-continental/sub-regional organizations which have proliferated over time without a centre which could coordinate them and give the whole picture a rational direction. This process has resulted in a messy system of overlapping integrative schemes with partially conflicting political and economic paradigms. This article analyzes the historical roots and drivers of this institutional disorder, focusing on the dynamics of unification and fragmentation under colonial rule, the political debates and the power politics among African states after their independence, the features of the African state system, and the role of external actors. The article also deals with the historical process of rationalization of the African integration system, comprising two interconnected dimensions: a horizontal one, which relates to the improvement of the institutional picture at the sub-regional level, and a vertical one, related to the relationship between the OAU/AU and sub-regional organizations.