| 40-man Roster | Root | Root's Root | Root^3 | Root^4 | How acquired | |
| 25-man Roster | Josh Beckett | Hanley Ramirez / Anibel Sanchez / Harvey Garcia / Jesus Delgado | Trade (2005) | |||
| Alex Cora | Ramon Vazquez | Dave Roberts | Henri Stanley | Trade (2005) | ||
| Brian Corey | Luis Mendoza | Trade (2006) | ||||
| Coco Crisp | Andy Marte / Guillermo Mota / Kelly Shoppach | Edgar Renteria / Hanley Ramirez / Anibel Sanchez / Harvey Garcia / Jesus Delgado | Trade (2006) | |||
| Manny Delcarmen | Second Round (2000) | |||||
| Alex Gonzalez | Free Agent (2006) | |||||
| Craig Hansen | Derek Lowe | Heathcliff Slocumb | Ken Ryan, Glenn Murray, Lee Tinsley | Derek Vinyard / Jim Smith | First Round (2005) | |
| Jason Johnson | PTBNL / cash | Trade (2006) | ||||
| Gabe Kapler | cash | Trade (2003) | ||||
| John Lester | Second Round (2002) | |||||
| Javier Lopez - C | PTBNL | Trade (2006) | ||||
| Mark Loretta | Doug Mirabelli | Justin Duchscherer | Trade (2005) | |||
| Mike Lowell | Hanley Ramirez / Anibel Sanchez / Harvey Garcia / Jesus Delgado | Trade (2005) | ||||
| Doug Mirabelli | Josh Bard / Cla Merideth | Andy Marte / Guillermo Mota / Kelly Shoppach | Edgar Renteria / Hanley Ramirez / Anibel Sanchez / Harvey Garcia / Jesus Delgado | Trade (2006) | ||
| David Ortiz | Free Agent (2003) | |||||
| Jonathan Papelbon | Fourth Round (2003) | |||||
| Wily Mo Pena | Bronson Arroyo | Waivers (Pirates) | Trade (2006) | |||
| Manny Ramirez | Free Agent (2000) | |||||
| Curt Schilling | Casey Fossum / Brandon Lyon / Jorge de la Rosa / Michael Goss | Mo Vaughn | Trade (2003) | |||
| Rudy Seanez | Free Agent (2005) | |||||
| Kyle Snyder | Royals | Waivers (2006) | ||||
| Julian Tavarez | Free Agent (2006) | |||||
| Mike Timlin | Free Agent (2003) | |||||
| David Wells | Free Agent (2004) | |||||
| Kevin Youkilis | Eighth Round (2001) | |||||
| DL | Matt Clement | Free Agent (2004) | ||||
| Lenny DiNardo | Mets | Rule 5 (2004) | ||||
| Kieth Foulke | Free Agent (2004) | |||||
| Trot Nixon | First Round (1993) | |||||
| Jason Varitek | Heathcliff Slocumb | Ken Ryan, Glenn Murray, Lee Tinsley | Derek Vinyard / Jim Smith | Trade (1997) | ||
| Tim Wakefield | Free Agent (1995) | |||||
| Minors | Abe Alvarez | Cliff Floyd | Sun-Woo Kim / Seung Song | Second Round (2003) | ||
| Craig Breslow | Free Agent (2006) | |||||
| Kason Gabbard | 29th Round (2000) | |||||
| Javier Lopez - P | David Riske | Andy Marte / Guillermo Mota / Kelly Shoppach | Edgar Renteria / Hanley Ramirez / Anibel Sanchez / Harvey Garcia / Jesus Delgado | Trade (2006) | ||
| Alejandro Machado | future considerations | Trade (2005) | ||||
| Edgar Martinez | Undrafted FA (1998) | |||||
| Brandon Moss | Eighth Round (2002) | |||||
| David Murphy | Ugueth Urbina | Tomo Okha / Rich Rundles | First Round (2003) | |||
| David Pauley | Dave Roberts | Henri Stanley | Trade (2004) | |||
| Adam Stern | Braves | Rule 5 (2005) | ||||
| Jermaine Van Buren | cash | Trade (2006) | ||||