Marcos debuted for Brazil in a match against Spain on November 13, 1999. Previously, he was included in Brazil’s squad for Copa América 1999 and 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 Copa América 2001 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 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 was elected the third-best goalkeeper in the tournament, as Brazil won the World Cup for the record fifth time. 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 2003 FIFA Confederations Cup and Copa América 2004. 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 October 6, 2005, Marcos announced his retirement from international football, but continued to play for Palmeiras, the only team he has played for in his career.