From here: Radio Baobab » Kyrgystan
In bishkek we applied for our Tajikistan visum and our GBAO permit. 60US$ + 50som per person. 3 days processing time. Visa is valid for 30 days. Ask specifically for a GBAO permit. The consul generally gives all regions, but make sure you check it (names are in LP). GBAO permit is free.
They keep your passport, make sure you have a photocopy of your passport. The consul then writes on the copy that your passport is in the embassy (you’ll need this on police checks)
The embassy was located here: N 42° 50,860 E 74° 37,756
Above information is from Sep 2007.
Enjoy Bishkek, nice town!