NL East | NL Central | NL West | AL East | AL Central | AL West
| Team | $ Val. | BA rank | BP rank | $ rank |
| Marlins | 148 | 2 | 5 | 1 |
| Braves | 144.4 | 6 | 4 | 2 |
| A's | 143.3 | 3 | 1 | 3 |
| Rangers | 127.4 | 1 | 2 | 4 |
| Rays | 113.2 | 4 | 3 | 5 |
| O's | 112.1 | 9 | 7 | 6 |
| Royals | 107.5 | 11 | 16 | 7 |
| Indians | 105.7 | 7 | 12 | 8 |
| Giants | 103.5 | 5 | 6 | 9 |
| Brewers | 99.7 | 10 | 15 | 10 |
| Red Sox | 99.2 | 13 | 8 | 11 |
| Cardinals | 98.9 | 8 | 9 | 12 |
| Yankees | 97.8 | 15 | 13 | 13 |
| Phillies | 95.6 | 12 | 14 | 14 |
| Twins | 94.3 | 22 | 20 | 15 |
| Blue Jays | 94.1 | 19 | 10 | 16 |
| Mariners | 85 | 24 | 17 | 17 |
| Mets | 83.5 | 17 | 18 | 18 |
| Reds | 78.5 | 14 | 19 | 19 |
| Pirates | 76.9 | 18 | 22 | 20 |
| D'Backs | 74 | 26 | 28 | 21 |
| White Sox | 72.06 | 16 | 24 | 22 |
| Rockies | 72.04 | 20 | 11 | 23 |
| Padres | 69.8 | 29 | 25 | 24 |
| Dodgers | 69.3 | 23 | 21 | 25 |
| Angels | 62.5 | 25 | 23 | 26 |
| Nationals | 58.4 | 21 | 29 | 27 |
| Cubs | 57.6 | 27 | 26 | 28 |
| Astros | 50.1 | 30 | 30 | 29 |
| Tigers | 45.1 | 28 | 27 | 30 |
$ Val. = Total team farm system surplus value.
BA Rank = Baseball America talent ranking for 2009.
BP Rank = Baseball Prospectus organizational ranking for 2009. (talent ranking, organizational ranking...same thing.)
The average farm system was $91.3M.