Veteran Paraguayan striker Roque Santa Cruz came through the youth system at Olimpia in his home country before making his debut for the team in 1997. In his two years with Olimpia at the start of his career, Roque Santa Cruz scored 13 goals in 24 league appearances.
Roque Santa Cruz made his Champions League debut in the colours of Bayern Munich during the 2-1 win over Dutch team PSV Eindhoven on September 15, 1999. His first goal in the Champions League came in his fifth appearance in the competition during the 2-1 loss to PSV Eindhoven and he was responsible for the only Bayern Munich goal having come on as a 26th minute substitute for Paulo Sergio. His goal came six minutes into the second half.
In his first season as a Bayern Munich player, Roque Santa Cruz helped the club win the league netting five goals in 28 appearances. He also helped Bayern Munich reach the last four of the Champions League. In total, he scored nine times in 48 games in all competitions during his debut season.