Stenson developed a formidable partnership with Justin Rose on day one yesterday, winning matches with the Englishman in both fourballs and foursomes.
He is also out with Rose this morning, but that looks likely to be his final match before tomorrow's singles.
"We've a little bit of an issue with Henrik at the moment," McGinley told Sky Sports News.
"He's got a tight back after playing so much golf so we're monitoring him for this afternoon."
Europe led 5-3 after the first day's play at Gleneagles.
Follow the morning fourballs on Saturday with our up-to-the-minute live blog here.