The 2000–01 season saw a West Indian touring party and Gilchrist warmed up with consecutive first-class centuries for Western Australia. Captaining his Test team for the first time in place of the injured Steve Waugh in the Third Test in Adelaide. Gilchrist scored only 9 and 10 not out, but a ten-wicket haul from Colin Miller resulted in a hard-fought five-wicket victory for Australia. Gilchrist described the match as "the proudest moment of my career". Waugh resumed the captaincy on his return to the team for the Fourth and Fifth Tests, with the series finishing in a 5–0 whitewash. Gilchrist scored 241 runs at 48.20 with two fifties. In the ensuing ODI tournament, Gilchrist scored 326 runs at 36.22 with a top-score of 98 as the Australians won all ten matches.