We examined populations of bats hibernating in 50 abandoned mines in Michigan during the 3 years before and 4–6 years after arrival of the fungal disease white-nose syndrome. Overall size of the regional population fell by 89.9%. Myotis lucifugus (Little Brown Bat), which represented 90% of the pre-epidemic population, declined by 89.9%. Myotis septentrionalis (Northern Long-eared Bat) and Perimyotis subflavus (Tricolored Bat) decreased by 98.5% and 93.9%, respectively, and both species appear threatened with regional extinction. Eptesicus fuscus (Big Brown Bat), in contrast, increased by 11.7%. The disease also impacted social patterns, with the proportion of Little Brown Bats that were solitary during hibernation in 10 of the mines increasing from 23% to 46% after onset of the disease.