Hughes had to cut a bullpen session short on Monday at Yankee Stadium, representing a significant setback for a pitcher who appeared primed to begin a Minor League rehabilitation assignment later this week.
Yankees team physician Christopher Ahmad examined Hughes on Monday evening and has recommended the MRI exam, as well as tests for blood circulation.
"It'll certainly put my mind at ease," Hughes said. "Hopefully, everything's OK and it's just a matter of building more arm strength and getting over this hump. For right now, it's just what they feel is the right way to go."
Hughes said that there is still no pain in his right arm and shoulder, only describing a feeling of deadness and fatigue. As a result, he said there wasn't much to take from Ahmad's visit.
"It's hard [to determine anything] through just a physical examination," Hughes said. "The strength tests and everything were fine. There's no real definitive test just by looking at it that you can do."
Hughes has been on the disabled list since April 15 with what has been officially listed as inflammation in his right shoulder, but since he had felt no pain, the Yankees resisted sending Hughes for an MRI exam.
"Usually, if a guy says he has pain, you go for an MRI," Yankees manager Joe Girardi said. "He just said he felt like it was dead and there wasn't a lot coming out. We figured that maybe he needed to be built up. We put him on a program, and now that the program didn't seem to work, we go get an MRI. He still says he's not experiencing pain."
The biggest issue is that Hughes has been unable to maintain his velocity, something he realized was continuing after throwing only 10 or 12 pitches on Monday.
The Yankees had been encouraged enough by Hughes' progress that they discussed scheduling a potential Minor League rehab start, which could have come on Thursday for Triple-A Scranton/Wilkes-Barre if Hughes' bullpen session had gone well.
Hughes felt no ill effects after throwing three 15-pitch "innings" in a bullpen session on Saturday in Baltimore, but he was unable to bounce back as anticipated.
"The first few felt all right, and then there was nothing there," Hughes said. "It's sort of the feeling you get after 110, 115 pitches -- I normally should feel that way. It's way too soon."
Hughes further compared the feeling in his shoulder with the numbness that sets in after being punched.
With Hughes out indefinitely, the Yankees will continue to look for contributions from their fill-ins.
Bartolo Colon and Freddy Garcia have both pitched well in the rotation, while veteran Kevin Millwood is also waiting in the wings at the Minor League level.
"No rotation ever wants to lose a starter," Girardi said. "Starters are something that are a premium. You've got a guy that wins 17 games as a starter last year, 18 total, and it's not easy to replace.
"Fortunately, we've had some guys that have thrown the ball well in Freddy and Bartolo. They're going to have to step up for us."
Bryan Hoch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.