The proliferation of Regional Trade Agreements (RTAs) has not spared the African Continent. The formation of RTAs in Africa is championed by the Regional Integration Agenda under the auspices of the Regional Economic Communities. The challenges that customs administrations face when their countries become members of RTAs depend on whether the RTA is trade-creating or trade-diverting. It is the trade-creating RTA that presents the customs administration with the greater challenges. This paper looks at these challenges and the areas where they require customs administrations to concentrate their policies and strategies.