The New York Mets of Major League Baseball (MLB) signed Pérez as a free agent in 2000. A September 1 callup, he made his MLB debut on September 1 against the St. Louis Cardinals. He singled to center field as a pinch hitter against Cardinals reliever Dave Veres and was then thrown out trying to steal second. He hit a combined 12-for-40 in the 2000 National League Division Series and 2000 National League Championship Series.