The pool stage of the 2008–09 Heineken Cup began on 10 October 2008, with the final match played on 25 January 2009.

The brackets show each team's ERC Ranking before the start of the 2008–2009 season.

The draw for the pool stage took place on 17 June 2008 in Dublin.

[1] The draw for the pool stages took place on 17 June 2008 in Dublin.

The runners-up are similarly sorted, and the best two are seeded seven and eight and progress to the quarter-finals alongside the six winners.