Kazuo Matsui
In January 2005, Hernández was traded to the New York Mets for catcher Vance Wilson. With the Mets out of playoff contention in and Hernández hitting over .300 in both Double-A and Triple-A, he was called up to the majors in mid-September but went 0-for-14 before finally getting his first hit, off Colorado Rockies pitcher Aaron Cook, in the last game of the season, going 1–4. Due to the knee injury of Kazuo Matsui, Hernández was the starting second baseman for the Mets to start the season, but he too was soon injured and placed on the 15-day DL. He returned later in the season and hit his first Major League home run on September 19, 2006, off Florida Marlins pitcher Scott Olsen. He is widely known to Mets fans for pinch-running for Paul LoDuca in the bottom of the ninth inning in Game 7 of the 2006 NLCS against the St. Louis Cardinals, representing the winning run with two out, but Carlos Beltrán struck out to end the game. In 2007, he made many appearances as a pinch-runner or a late inning defensive replacement, as he only collected three at-bats and went 1–3. On August 20, , Hernández was dealt to the Washington Nationals as a player to be named later for relief pitcher Luis Ayala.