"The one big injury we have got, unfortunately, is Ryan Shawcross who's pulled up in training and is likely to miss certainly the weekend," Hughes told a news conference on Friday.
"It's not what he's had before in terms of disc injuries, it's ligaments around the back and we have to wait for him to settle down. It's unfortunate because he's started the season really well."
Cameroon winger Eric Maxim Choupo-Moting is also a doubt after injuring a hamstring on international duty, while several other players are carrying minor knocks.
United have not won at Stoke in the league since April 2013, but are the early pace-setters in the league, topping the table after winning all three of their matches so far with 10 goals scored and none conceded.
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"Of all the teams they are clearly at the top of the pile," said Hughes, whose team went down to Everton, beat Arsenal and drew with West Bromwich Albion in their first three matches.
"(United's) performances and the way they've gone about their business has been impressive," Hughes added.
"We had a similar situation last year with Man City, who were not able to sustain it, but the make up of the Man United squad is very strong and they're playing in a way that their fans will take to and enjoy.
"They expect teams to attack with power and pace and ability. It's very early days. Hopefully there are still things for us to exploit."
(Reporting by Shrivathsa Sridhar in Bengaluru; editing by Amlan Chakraborty)
