Marcos debuted for
Brazil in a match against
Spain on 13 November 1999. Previously, he was included in Brazil's squad for the
1999 Copa América and the
1999 FIFA Confederations Cup as a second-choice goalkeeper. He remained as Brazil's backup goalkeeper as
Dida and
Rogério Ceni were preferred ahead of him. He became Brazil's starting goalkeeper in the
2001 Copa América and retained that position after the tournament, relegating Dida to the bench. He was subsequently included in Brazil's squad for
2002 FIFA World Cup as the first-choice goalkeeper, replacing
Cláudio Taffarel. He started every game in the tournament and played every minute of Brazil's matches in the tournament. He had four clean sheets, conceded only four goals in seven matches, and helped Brazil win the World Cup for a record fifth time.
Simon Kuper and Stefan Szymanski reported in their book
Soccernomics that Marcos spent the entire tournament in severe pain from a prior broken wrist injury that did not properly heal, unable to train fully or even catch the ball in some matches. According to Marcos' agent, Marcos hid the injury from manager
Luiz Felipe Scolari through the tournament. However, after a series of injuries that affected his career, Marcos lost his place in the team after the World Cup. He made only four more international appearances after the World Cup, and was left out of Brazil's squad for the
2003 FIFA Confederations Cup and the
2004 Copa América. In 2005, he was called again and included in the squad for the
2005 FIFA Confederations Cup. He made one appearance in the tournament, starting in a 2–2 draw against
Japan during the group stage, which turned out to be his last appearance for Brazil. On 6 October 2005, Marcos announced his retirement from international football, but continued to play for Palmeiras, the only team he has played for in his career. However, he would later go back on his decision to retire from the national team, and announced himself as still available for selection. He was placed on standby lists for the
2006 FIFA World Cup and the
2007 Copa América, but did not manage to get a place in the final list of either competitions. ==Style of play==