It was suggested Gilberto was less than impressed at Wenger's demands he play at centre-half and was set to be left out of tonight's Carling Cup tie with Sheffield United as a result, fuelling speculation he could be set to leave when the transfer window opens in January.
Wenger, however, denied a bust-up with the 2002 World Cup winner.
"I deny that categorically," he told Arsenal TV Online.
"I find this assessment disrespectful to a great professional like Gilberto. He is 100% professional and is in the squad for tomorrow. He will play."
Wenger continued: "I believe that as a manager and as a player you always have one thing in your mind and that is what is good for the club and the team and I cannot fault Gilberto on that since he arrived here.
"Recently he has played less, but his mentality has been superb.
"It is important to win every single competition and in this one I use younger players because traditionally it has always been like that and it has helped us a lot to develop the players."