In 2003–06, targeted (active) surveillance for European bat lyssaviruses (EBLVs) was undertaken throughout England, focusing on two species most likely to host these viruses, Myotis daubentonii and Eptesicus serotinus. Blood was sampled for the detection of EBLV-specific neutralizing antibodies and oropharyngeal swabs were taken for the detection of viral RNA or infectious virus in saliva. Between 2003 and 2006, 273 E. serotinus and 363 M. daubentonii blood samples were tested by the EBLV-1 or EBLV-2 specific modified fluorescent antibody neutralization test. The EBLV-2 antibody prevalence estimate was 1.0–4.1% (95% confidence interval [CI]; mean=2.2%) for M. daubentonii. European bat lyssavirus type 1–specific antibodies were detected only in a single E. serotinus. Other nontarget species (n=5) were sampled in small numbers (n=24), with no EBLV-specific antibody detected. No viral RNA or live virus was detected in any of the oropharyngeal swabs analyzed. Host RNA was detected from 83% of the oropharyngeal swabs analyzed (total swabs 2003–06: n=766). These data show that EBLV-2 is present in M. daubentonii in England. In contrast, there is insufficient evidence to suggest that EBLV-1 is present in E. serotinus in England, although further research is warranted.