The Italian was unhappy that Wigan midfielder and the Stoke pair did not report for Carling Nations Cup duty in May, and he saw them withdraw from the squad once again for the friendly clash with Croatia earlier this month.
In whittling his initial squad down to 25 today, he made his feelings abundantly clear, although McCarthy has been made available for selection for the Under-21s and could yet return to contention should he be required.
Trapattoni said: "Picking the final 25 players for the squad has not been an easy task, and unfortunately some players have been left out.
"We will continue to monitor their progress with their clubs and call them up if necessary.''
Wigan were adamant McCarthy was struggling with an ankle injury when he initially failed to meet up with the Ireland squad. However, former Italy manager Trapattoni believes all players should report even if they are injured so they can be assessed by medical staff.
Defenders Paul McShane and Seamus Coleman are also missing, but they have been left out because of injury.
Sunderland defender John O'Shea is included despite having yet to play a competitive game for his new club because of a hamstring problem picked up during pre-season.
Ireland face Slovakia at the Aviva Stadium on September 2 and Russia in Moscow four days later in a double-header which could well determine the outcome of Group B.
The three sides are currently locked together at the top of the group on 13 points.
Russia won 3-2 in Dublin on October 8, but Trapattoni's men bounced back from that disappointment to claim a point in Slovakia four days later.
Home and away victories over Macedonia since have kept the Republic firmly in the race for qualification for the finals of a major tournament for the first time since the 2002 World Cup in the Far East with Russian managing only a draw in Armenia in March.
Squad: Given (Aston Villa), Westwood (Sunderland), Forde (Millwall), O'Shea (Sunderland), Foley (Wolves), Kelly (Fulham), Ward (Wolves), Dunne (Aston Villa), Kilbane (Derby), St Ledger (Leicester), O'Dea (Leeds), Whelan (Stoke), Gibson (Manchester United), Andrews (Ipswich), Fahey (Birmingham), Keogh (Leeds), Duff (Fulham), McGeady (Spartak Moscow), Hunt (Wolves), Lawrence (Portsmouth), Treacy (Burnley), Keane (Los Angeles Galaxy), Doyle (Wolves), Long (West Brom), Cox (West Brom).