Marquis will have the surgery Friday in Cincinnati. Dr. Tim Kremchek will perform the procedure.
Once he has the surgery, Marquis is expected to be back on the mound sometime in August. Marquis said when he woke up Wednesday morning, he realized that his elbow was in pain and had locked up on him.
"We have to see where we go from here and talk it over with the team, my agent and my family -- see what the best plan is," he said. "I let my teammates down, but they are doing a great job. We have a lot of quality guys in here. Hopefully I could come back in August and contribute."
Marquis signed a two-year, $15 million deal with the Washington in the offseason. He got off to a slow start, allowing 19 earned runs in 8 1/3 innings. The Nats began to believe that something was wrong with Marquis on April 18, when he didn't record an out and allowed seven earned runs against the Brewers.
A few days later, Marquis had an MRI and it was revealed that he had bone chips and spurs in the elbow. Marquis tried to avoid surgery. He was able to play catch and have bullpen sessions without any problems.
"It was an agreement between the player and us," general manager Mike Rizzo said. "He felt that he could pitch through it. He felt these things before and has pitched through it. We wanted to do what was best for the player. It was a mutual decision to try to let him pitch through it. It didn't work, so it set us back for about three weeks."
Marquis acknowledged that he didn't feel comfortable in his rehab start for Potomac on Tuesday. He allowed three runs in 3 2/3 innings in an 8-5 loss to Winston-Salem. Marquis threw 54 pitches, 36 for strikes. His fastball was clocked at 88 mph, which concerned the team.
"It was cold; it was tough to stay loose," Marquis said. "So I thought it was -- maybe more than anything -- why the elbow was a little stiff. I tried to stay warm and do everything that I could. Now realizing what my arm feels like this morning, if it was 85 degrees and sunny, I think it would probably be the same thing."