| New York Mets |
| Updated | Player | Pos | Injury | Expected Return |
| 12/15/08 | Darren O'Day | RP | Shoulder | Might be out for the 2009 season |
| 11/20/08 | Daniel Murphy | LF | Hamstring | Hoping to be ready for spring training |
| 11/04/08 | John Maine | SP | Shoulder | Hoping to be ready for spring training |
| 11/03/08 | Tony Armas | SP | Hernia | Free agent. Expected to be ready for spring training |
| 11/03/08 | Orlando Hernandez | SP | Foot | Free agent. Hoping to be ready for spring training |
| 10/31/08 | Moises Alou | LF | Hamstring | Free agent. Might retire |
| 10/31/08 | Damion Easley | 2B | Quadriceps | Free agent. Expected to be ready for spring training |
| 10/31/08 | Matt Wise | RP | Shoulder | Free agent. Hoping to be ready for spring training |
| 12/15/08 | Ambiorix Burgos | RP | Elbow, personal | Free agent. Might retire |
| 12/02/08 | Nick Evans | LF | Quadriceps | Hoping to be ready for spring training |
| 11/04/08 | Angel Pagan | LF | Shoulder | Hoping to be ready for spring training |
| 10/01/08 | Johan Santana | SP | Knee | Expected to be ready for spring training |
| 10/31/08 | Fernando Tatis | LF | Shoulder | Expected to be ready for spring training |
| 10/15/08 | Billy Wagner | RP | Elbow | Out for the 2009 season |