This study examines mercury exposure in bats across the northeast U.S. from 2005 to 2009. We collected 1,481 fur and 681 blood samples from 8 states and analyzed them for total Hg. A subset (n = 20) are also analyzed for methylmercury (MeHg). Ten species of bats from the northeast U.S. are represented in this study of which two are protected by the Endangered Species Act (ESA 1973) and two other species are pending review. There are four objectives in this paper: (1) to examine correlates to differences in fur–Hg levels among all of the sampling sites, including age, sex, species, and presence of a Hg point source; (2) define the relationship between blood and fur–Hg levels and the factors that influence that relationship including age, sex, species, reproductive status, and energetic condition; (3) determine the relationships between total Hg and MeHg in five common eastern bat species; and (4) assess the distribution of Hg across bat populations in the northeast. We found total blood and fur mercury was eight times higher in bats captured near point sources compared to nonpoint sources. Blood–Hg and fur–Hg were well correlated with females on average accumulating two times more Hg in fur than males. On average fur MeHg accounted for 86 % (range 71–95 %) of the total Hg in bat fur. Considering that females had high Hg concentrations, beyond that of established levels of concern, suggests there could be negative implications for bat populations from high Hg exposure since Hg is readily transferred to pups via breast milk. Bats provide an integral part of the ecosystem and their protection is considered to be of high priority. More research is needed to determine if Hg is a stressor that is negatively impacting bat populations.