Senator Tim Johnson narrowly won re-election to a second term over Republican John Thune by a margin of 524 votes, or 0.15%.

Thune later narrowly won South Dakota's other U.S. Senate seat in 2004, and was re-elected in 2010, 2016, and 2022 in uncompetitive elections.

Thune launched a television advertising campaign mentioning al Qaeda and Saddam Hussein, contending that both are seeking nuclear weapons and that this country needs a missile defense system, something Johnson voted against 29 times and that Thune supports.

Johnson's narrow victory may be attributed to his strong support in Oglala Lakota County, and to Thune also underperforming in typically Republican areas.

Thune was elected to South Dakota's other Senate seat in 2004, defeating incumbent minority leader Tom Daschle.