I have a 1999 Regal GS that is not charging.
Brought the alternator to Autozone to be checked and it passed on thier machine. Any thought to what might be wrong or how I should trouble shoot the problem? I disconnect the ground on the battery with the engine running and it stalls right out. Usually this means the alternator is bad.
What else could cause it not to charge?

It is a VERY bad idea to disconnect a battery cable on an OBD-II vehicle when it is running. It can (and most often will) short out very expensive electronics like the PCM and EBCM. Most often, the car will die regardless of the charging system's condition as a safety/system protection in the PCM's prgramming. The best way to check is to use a DMM to check system voltage. With the car running, it should be 13.8-15.2 volts. Battery voltage should be 12.6-13.2 volts with the engine and all accessories off.

check fuses & fuesable links do you have battery voltage at alt??