Martínez was acquired by the Boston Red Sox as a non-drafted free agent in 1997. The Red Sox assigned Martínez to the Gulf Coast Red Sox, their Rookie-level minor league affiliate, where in 1998 he made ten starts, posting a 2-3 record with an ERA of 3.18. The club promoted him to the Single-A Lowell Spinners for the 1999 season, where he went 0-3 with a 3.68 ERA before being promoted to the Single-A Augusta GreenJackets. While Martínez initially struggled at Augusta; over the next two seasons (1999–2000) he went 11-10 with an ERA of 5.96. Martínez improved however, and at the end of the 2000 season narrowly missed pitching a no-hitter, giving up a one-out single in the 9th inning against the Asheville Tourists. Martínez\'s performance came just two days after teammate Eric Glaser threw a no-hitter against the Hagerstown Suns.\n', '

In 2001 the Red Sox promoted Martínez to the High-A Sarasota Red Sox where he went 9-12 with an ERA of 3.35. Following the 2001 season the Red Sox placed Martínez on their 40-man roster and promoted him to the Double-A Trenton Thunder. Following spring training Martínez spent the entirety of the 2002 season with Trenton, going 5-12 with a 5.31 ERA. One sportswriter, who considered Martínez a top prospect, said that Martínez showed "flashes of brilliance but also considerable inconsistency at Trenton."\n', '

Martínez began what would be prove to be an unusual 2003 season with the Triple-A Pawtucket Red Sox, but the Red Sox soon moved him down to the Double-A Portland Sea Dogs, intending to convert him into a closer. In 34 relief appearances with Portland Martínez posted a 3-1 record with 14 saves and a 2.25 ERA. On July 22, 2003, the Red Sox traded Martínez and Brandon Lyon to the Pittsburgh Pirates for Scott Sauerbeck and Mike González. The Pirates assigned Martínez to the Double-A Altoona Curve, where he made three relief appearances before, in a strange twist, the Pirates sent him and Lyon right back to Boston on August 1, along with Jeff Suppan, while Boston returned Gonzalez while adding Freddy Sanchez. The Pirates had raised concerns over the state of Lyon\'s elbow (Lyon would miss the entire 2004 season); the new trade effectively canceled the old one. Martínez finished out the season at Pawtucket.\n', '

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