Sauk and Mesquakie society was part patrilineal and part matrilineal. Sons usually inherited their father's title and function, yet ancestry was traced along matrilineal lines. No matter what ethnic group a person's father belonged to, he or she automatically belonged to his or her mother's clan. Women also played an important part in tribal government. The son of a civil chief could not inherit his father's title unless the women of the community approved of him first.

Children were born into extended families called clans. The guardian spirit of the clan members' common ancestor distinguished clans. There were wolf, elk, bear, swan, sturgeon, bald eagle, and even snow and thunder clans.

This function was passed down from father to eldest son. The civil chief settled disputes within the tribe. He led discussions at tribal council meetings. He also played a diplomatic role, representing his people at councils with other tribes. In wartime, the civil chief deferred to the war chief.

In wartime, the council selected a war chief from among the bravest and ablest of the warriors. The war chief presided over council meetings whenever war-related topics were discussed. He also acted as a general, leading the tribe's warriors during military campaigns.

Whenever an important decision had to be made, the civil chief called the tribe's clan chiefs together for a council meeting. Decisions were made by consensus. Skilled orators were much admired and could speak untiringly for many hours. On questions of war and peace, talks could go on for several days, or weeks. It was up to the civil chief to get the people to comply with the council's decisions. He could not force the people to obey. He had to persuade them. On occasion, a dissenting minority might move to another village.

The tribal council selected the ceremonial chief from among the village's most highly regarded medicine men or shamans. Primarily the keeper of the religious rites, the ceremonial chief instructed others in the various rituals of the tribe.

The American government disrupted the Sauk and Mesquakie's traditional manner of selecting chiefs and governing themselves. Beginning during the time of the War of 1812, the U.S. considered the more compliant Keokuk as the Sauk and Mesquakie's civil chief and refused to deal with the tribes' hereditary chiefs. Today, each Sauk and Mesquakie band elects a tribal council modelled after the U.S. system of government.