Loan keeper Kamil Grabara and attacking midfielder Alex Pritchard was not involved in Wednesday's goalless draw with fellow Championship strugglers Middlesbrough due to illness and they will be assessed in the build-up to Saturday's game.
Other players have also been feeling 'under the weather' in the past week, including Karlan Grant and Adama Diahkaby.
Cowley is hoping that the picture clears ahead of the visit of a Barnsley side who he was very impressed with in Tuesday night's draw at West Brom.
He said: "For us, if we can get well, that will be good. We will obviously have a day's less recovery than Barnsley, which will be a challenge.
"But we are at home and we love being at home and it is a Yorkshire derby and I am looking forward to that."
Reflecting on the Boro performance, he added: "We will dust ourselves off, learn lots and take that forward into a Barnsley game on Saturday where we anticipate another team playing a back five.
"I watched them at West Brom and they played really, really well and were really aggressive.
"It will be another tough game, for sure. Barnsley will come and play in a really similar way and the challenge for us now is to go back to the game plan and look at what it was and compare to how we executed and performed and try to work out what we can do better going into Saturday."