Nady made two throws from right field during an International League game at Syracuse, feeling significant discomfort in his right elbow after the second one and leaving the game.
Yankees manager Joe Girardi exchanged text messages with Nady, who will fly to California and visit on Tuesday with Dr. Lewis Yocum, the noted surgeon who performed Nady's original September 2001 Tommy John surgery.
A repeat procedure would wipe out Nady's 2009 season and take approximately 12 to 18 months for full recovery. Nady is in his final year under contract with the Yankees.
"My gut tells me it's injured again, but I can't tell you that for sure until he visits with them," Girardi said. "The fact that he's going out to see Dr. Yocum tells me it's more than what he felt in Tampa."
Nady was originally injured in an April 14 game at Tropicana Field, feeling sharp pain before being diagnosed with a ligament tear in his right elbow as he returned a routine hit to the infield.
A first diagnosis recommended surgery, but Nady instead attempted to rehab the injury in Tampa, Fla., after receiving a pair of plasma injections intended to assist with healing.
"It's disappointing," Girardi said. "I'm more disappointed for him than myself. Obviously, as a club, you would love to have him back. He was very good for us last year.
"I'm really disappointed for him because he's put a lot of time into this. If it comes to where there's something that needs to be repaired, the 2 1/2 months he spent trying to rehab it, I feel very bad for him."
Nady, 30, hit .286 (8-for-28) in seven games for the Yankees this season after beating out Nick Swisher to be New York's Opening Day right fielder.
The 2009 season would have been Nady's first full year in pinstripes. He was acquired last July from the Pirates and batted .268 with 12 home runs and 40 RBIs in 59 games the rest of the season.
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.