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Gilchrist brought up his ton in 98 minutes with a two off Steve Harmison late on the third day at the WACA.
Gilchrist just missed the world record of 56 balls set by West Indian Viv Richards against England at St. Johns in 1985-86.
However, he eclipsed the previous second best mark of 67 balls set by Australia's Jack Gregory against South Africa in Johannesburg in 1921-22.
Gilchrist also broke the record for the most runs in a six-ball over in an Ashes series when he plundered 24 off Monty Panesar.