Clayton County is a county located in the U.S. state of Iowa. The population was 18,129 in the 2010 census, a decline from 18,678 in 2000. Its county seat is Elkader.

According to the 2000 census, the county has a total area of 792.81 square miles, of which 778.81 square miles or 98.23% is land and 14.00 square miles or 1.77% is water.

Clayton County is part of the Driftless Area, a region that completely missed being ice-covered during the last ice age. Streams have deeply carved valleys, while the Mississippi River has spectacular bluffs.

Clayton County was established on December 21, 1837 when it split from Dubuque County. It was named in honor of John Middleton Clayton. Clayton was a lawyer, politician, and U.S. Senator from Delaware. He later served as Secretary of State under President Zachary Taylor.

The county seat of Clayton County moved several times between 1840 and 1876. It was located first in Prairie La Porte, but in 1843 the people voted to have the seat changed to Jacksonville. Later, the county seat moved to Garnavillo and then to Elkader. As soon as Elkader was declared the county seat, the city of Guttenberg petitioned to consider an election between Elkader and Guttenberg. Guttenberg won the election by 1,007 votes. Just as the county records were arriving in Guttenberg, Garnavillo moved to have the county seat relocated. Several other contests between these cities followed, but eventually Elkader was victorious in securing the county seat.

The first courthouse was built in Prairie La Porte in 1840, now known as Guttenburg. The second courthouse was built in 1844 in Jacksonville, later renamed to Garnavillo. This building was sold in 1866 to help fund a courthouse to be built in the new county seat of Elkader. The County Board of Supervisors could only spend $2,000 a year on construction of the Elkader courthouse. However, by 1876, with another county seat contest pressing, the citizens of Elkader and the county came up with the $10,000 needed for the courthouse.

The present courthouse, designed with Italianate architectural style by O.F. Davis, was begun in the summer of 1867. A large addition to the original building was added in 1877. This red brick building used limestone quarried nearby for the foundation. The courthouse was listed on the National Register of Historic Places in 1976 as a part of the County Courthouses in Iowa Thematic Resource. The cornerstone, laid in 1887, reads "July 4, A.L. 5877." The A.L. stands for Anno Lucis, or Year of Light, a date used by Freemasons to indicate the number of years that have elapsed since 4000 B.C.

Spacious additions and a clock tower have been added as well as a Civil War monument that was added to the grounds in 1919. The clock is a Howard clock model #1, records indicate its installation was in 1890. The clock was paid for by the citizens of Elkader. The clock required daily winding, then was electrified in 1980. The cupola was expanded in 1896 to include a 45-foot clock tower.