BOSTON — Rebuilding the Boston Red Sox began a few years ago for general manager Theo Epstein & Co.

The organization made a commitment to redevelop its minor-league system to create a prosperous future.

Boston’s philosophy has come to fruition and yesterday was another step to make sure the Red Sox are perennial winners for a long time.

Second baseman Dustin Pedroia, 25, signed a six-year contract worth $40.5 million in what is sure to be the first of many long-term deals the Red Sox will give to their core of young talent.

“If we had 25 guys like Dustin, we would be in good shape,” Epstein said during yesterday’s press conference at Fenway Park.

Not everyone can be like Pedroia, but the rest of the Sox’ talent is special in their own right, leaving the organization no choice but to sign these players for the long term.

Kevin Youkilis, Jonathan Papelbon, Jon Lester, Jacoby Ellsbury and Jed Lowrie are all players the Red Sox would like to have under control for the near future and beyond.

“We hope so,” Epstein said. “We said the first day of the offseason it was a goal of ours to sign certain players to long-term deals. We’re not going to discuss who or where or when, but I’ll say Dustin is not the only player we’re talking to this winter. It’s significant now that he’s signed and maybe it can create some momentum.”

Jason Bay is not a homegrown guy, but the 30-year-old outfielder is also expected to sign a new deal with the Red Sox since his current contract expires after the 2009 season.

Epstein and the Red Sox vision began in 2002 and their tireless work and dedication with the amateur draft in subsequent years have paid huge dividends for the organization. Pedroia, Papelbon, Ellsbury and pitcher Clay Buchholz are all products of the 2003, 2004, and 2005 drafts under Epstein.

All have worked their way through the successful minor-league system, and all have made significant contributions for the Sox en route to the World Series championship in 2007.

Pedroia has only two full seasons of major-league experience, but already he’s become a leader on and off the field. That’s the reason the Red Sox want him, and others, under lock and key for a long time.

“He embodies everything we look for in a Red Sox player,” Epstein said of Pedroia. “This is a great day for the organization. … He’s a part of this core of young players that we have moving forward. He’s a leader of that core of young players that we have. I would like to think that group is going to be together for a long time and win some championships for the city.”

Normally when the Red Sox hold a press conference to announce a signing there are only a few club personnel on hand. That wasn’t the case for Pedroia yesterday. Members of the organization’s scouting and front-office departments, along with medical and minor and major league staffs were all on hand to show their support for Pedroia.

“We take some additional pride as an organization that Dustin was drafted by the Red Sox and came up through our system,” Epstein said. “This is the only organization he’s ever known. It’s an appropriate time to tip our cap to our scouting department and player-development department for helping Dustin get where he is today.”

The spunk, grit and leadership that Pedroia embodies — and Epstein spoke eloquently of — are exactly the type of team the Red Sox want. Even off the field Pedroia displays his confidence, and that was evident during his press conference yesterday afternoon.

He was asked whether he thinks about what he has accomplished in only two full seasons in the majors, and how people doubted his abilities after the first month of his rookie season.

“I think about that all the time. I think you guys are all stupid for not believing in me,” he said with a smile. “I’m just kidding. I do think about that stuff, and it just shows if you work as hard as you can, that you can fit in any environment and be successful.”

It won’t be long before the Red Sox follow up Pedroia’s contract with others like it to other deserving players.

jmcdonal@projo.com