Duffy recently filed as a Minor League free agent, effectively ending an up-and-down relationship with the organization that drafted him in the eighth round of the 2001 First-Year Player Draft.
"I think Chris wants to explore other options, and we agree that that might be the best thing for him right now," general manager Neal Huntington said.
The Pirates, still holding out hope that Duffy could reemerge as an option in the outfield at the Major League level, sent the outfielder to Mexico for winter ball. After playing in three games, however, Duffy abruptly left his Mazatlan team.
"He just didn't want to be there," Huntington explained. "The information that I have is that he just shut it down."
After leaving Mexico, Duffy filed for free agency and informed the Pirates that he would explore playing elsewhere. He expressed no desire to return to the Pittsburgh organization.
"I think he realized that he had fallen behind a number of players in the organization," Huntington said. "We wish him the best, but the reality is that players have moved in front him, and he knows that."
As Duffy dealt with injuries and untapped expectations, he certainly fell back in an organization that arguably has more depth at the outfield position than at any other. Nyjer Morgan and Steve Pearce both ascended from Triple-A to the Majors this past season, and it's just a matter of time before top prospects Andrew McCutchen and Jose Tabata also arrive in Pittsburgh.
Duffy spent much of the season recovering from the shoulder surgery he underwent in August 2007. In all, he appeared in 30 games combined at Double-A Altoona and Triple-A Indianapolis in '08. The 28-year-old finished with a .266 average, two home runs, 10 RBIs and six stolen bases.
He was the team's Opening Day center fielder in 2006 and played with the Pirates in parts of three seasons. His career numbers with the Pirates: a .269 average, 49 RBIs and 41 stolen bases over 193 games.
Duffy is just one of a number of players within the organization to declare Minor League free agency. Others include pitcher Franquelis Osoria, infielders Melvin Dorta, Luis Ordaz, Luis Cruz and Matt Kata and catchers Miguel Perez and Carlos Maldonado.
The Pirates also recently added pitcher Evan Meek to the club's 40-man roster in order to prevent him from being able to file for Minor League free agency.
Jenifer Langosch is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.