This distinctive means that every local New Testament church has the privilege to be in total control of itself. In the autonomous form of church government, the system of authority rests in an independent, indigenous, self-propagating, self-supporting, and self-governing local church. This Baptist distinctive distinguishes itself from two other forms of church government, the Episcopalian, and Presbyterian.
The Episcopalian form of church government places its authority in a system of priests and bishops in an ascending scale. For example, in the Roman Church, the ultimate authority rests in the supreme pontiff, the pope.
The Presbyterian form of church government places its authority in a representative group called preaching and ruling elders.
In this way delegated authority finds its final authority in the highest group. For this process of delegated authority rises in an ascending order from the local church session to the presbytery to the state synod until it finally rests in the General Assembly which is natural.
(From William Kerr, Conservative Baptist Distinctives, Portland, OR: Christianews Press, 1962, pp. 8-10)