The objective of this study was to describe rates of religious vaccination exemptions over time and the association with pertussis in New York State (NYS).METHODS:Religious vaccination exemptions reported via school surveys of the NYS Department of Health from 2000 through 2011 were reviewed by county, and the changes were assessed against incidence rates of pertussis among children reported to the NYS Department of Health Communicable Disease Electronic Surveillance System.RESULTS:The overall annual state mean prevalence (± SD) of religious exemptions for ≥1 vaccines in 2000-2011 was 0.4% ± 0.08% and increased significantly from 0.23% in 2000 to 0.45% in 2011 (P = .001). The prevalence of religious exemptions varied greatly among counties and increased by >100% in 34 counties during the study period. Counties with mean exemption prevalence rates of ≥1% reported a higher incidence of pertussis, 33 per 100 000 than counties with lower exemption rates, 20 per 100 000, P < .001. In addition, the risk of pertussis among vaccinated children living in counties with high exemption rate increased with increase of exemption rate among exempted children (P = .008).CONCLUSIONS:The prevalence of religious exemptions varies among NYS counties and increased during the past decade. Counties with higher exemption rates had higher rates of reported pertussis among exempted and vaccinated children when compared with the low-exemption counties. More studies are needed to characterize differences in the process of obtaining exemptions among NYS schools, and education is needed regarding the risks to the community of individuals opting out from recommended vaccinations.