Boggs was re-elected to the House in 1946 and continued to serve there until his death. He ran an unsuccessful race for the governorship of Louisiana in 1952. During his tenure in Congress Boggs was instrumental in passage of interstate highway program in 1956, and was a member of the Warren Commission in 1963-4. He served as Democratic House whip from 1961-1970 and as majority leader (from January 1971).
While on a flight between Anchorage and Juneau, Alaska, Boggs' Cessna disappeared with three other people on board (Rep. Nick Begich of Alaska, Boggs' aide and the pilot). After the most intensive search ever conducted by the U.S. military, which lasted 39 days, no bodies were ever found. House Resolution 1 of January 3, 1973 acknowledged Boggs' death and opened the way for a special election.
In 1973 Boggs' wife, Lindy, was elected to the second district seat left vacant by his death. They are the parents of television commentator Cokie Roberts, attorney Thomas Hale Boggs, Jr, and Barbara Boggs Sigmund.