Eight teams, specifically the six pool winners and the two best runners-up, qualified for the quarter-finals, starting a knock-out phase that will end with the final at Stade de France in the Paris suburb of Saint-Denis.

For the first time, the third- through fifth-ranking runners-up parachuted into the knockout stage of the European Challenge Cup.

[1] Also for the first time, the winner of the Heineken Cup will receive an automatic berth in the following season's competition.

[5] The brackets show each team's European Rugby Club Ranking at the start of the 2009–10 season.

These teams became the 5th through 7th seeds in the Challenge Cup knockout phase, and played their quarter-finals away.