| Active Minor League Home Run Leaders | |||
| Player | Debut | 2006 | Career |
| Izzy Alcantara | 1991 | 5 | 304 |
| Ernie Young | 1990 | 7 | 300 |
| Adam Hyzdu | 1990 | 7 | 266 |
| Mike Coolbaugh | 1990 | 0 | 250 |
| Kevin Witt | 1994 | 17 | 250 |
| Alan Zinter | 1989 | 3 | 241 |
| Chad Mottola | 1992 | 10 | 226 |
| Kit Pellow | 1996 | 16 | 214 |
| Scott McClain | 1990 | 10 | 213 |
| Mike Hessman | 1996 | 12 | 211 |
| Earl Snyder | 1998 | 11 | 201 |
| Aaron Guiel | 1993 | 7 | 200 |
| Rob Stratton | 1996 | 13 | 197 |
| Jon Nunnally | 1992 | 3 | 195 |
| Graham Koonce | 1994 | 3 | 181 |
| Kevin Barker | 1996 | 11 | 180 |
| Alejandro Freire | 1993 | 3 | 178 |
| Andy Tracy | 1996 | 10 | 176 |
| Chris Truby | 1993 | 3 | 174 |
| Jason Wood | 1991 | 9 | 174 |
| -Compiled by Matt Eddy | |||