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Lee County is a county located in the U.S. state of Iowa. It was established in 1836 and named for a family prominent in the New York Land Company, owners of extensive interests in the Half-Breed Tract in the 1830s.

As of 2000, the population was 38,052. Unlike most counties nationwide (including all other counties in Iowa), Lee has two county seats — Fort Madison and Keokuk. The latter was established in 1847 when disagreements led to a second court jurisdiction.

Regular sessions of the Board of Supervisors are held at 9 a.m. Tuesday mornings.