Michael Conroy / AP

Michael Phelps sets a record in the 100-meter butterfly at the U.S. Nationals on Thursday.

updated 9:51 a.m. ET July 10, 2009

INDIANAPOLIS - Michael Phelps withdrew from the 100-meter freestyle at the U.S. national championships Friday because of a sore neck.

The 14-time Olympic gold medalist was supposed to swim in the last morning heat, but he was still in pain after waking up a day earlier with a kink on the left side of his neck.

“It was worse this morning,” he said.

Phelps said he swam through the pain in setting a world record in the 100 butterfly Thursday night. He received numerous treatments on his neck both Thursday and Friday.

“It wasn’t fun swimming the 100 fly with that,” he said. “I could barely move my neck to breathe. I definitely didn’t feel 100 percent.”

The 100 free, in which Phelps owns the American record, was going to be his final event at nationals. Phelps said he was willing to try, but his coach Bob Bowman vetoed that idea after consulting with a doctor.

“We’re going to err on the safe side,” Bowman said.

Phelps has qualified for the world championships later this month in the 100 and 200 flys and the 200 free. It’s likely he will swim on three relays in Rome.

Even if he had qualified in the 100 free, Phelps said he wouldn’t have swum the event at worlds because it conflicts with the 200 fly. The swimming events begin July 26, giving him two weeks to train.

“There will be many more 100 free races to swim,” he said.

It’s not the first time Phelps has experienced bad luck in Indianapolis.

In October 2004, he withdrew from the world short course championships here because of a back injury that he blamed on traveling by bus and sitting for several hours during a post-Olympic promotional tour.

That April, he withdrew from three events at a meet here because of suspected food poisoning.