Follow exactly what Pete was saying above, with the following modifications/additions:

1) For safety, disconnect the negative battery terminal and put one probe of the ammeter on the battery terminal and one on the cable end. Make sure everything in the vehicle is shut off and the doors are closed.

2) If pulling one fuse at a time does not find your culprit, disconnect the alternator wires from the back of the alternator and see if the meter drops below 50 mA. If so, then you have found your problem.

When I go looking for these problems, I don't use the big expensive meter that can measure 10A. The little Radio Shack meter that is the size of a pack of cigarettes is much more convenient. It will measure up to 1A. Your current leak is certainly less than this amount (probably 100 to 500 mA).