Background Although incidence of vaccine-preventable diseases has decreased, states’ school immunization requirements are increasingly challenged. Subsequent to a federal court ruling affecting religious immunization exemptions to school requirements, new legislation made philosophical immunization exemptions available in Arkansas in 2003–2004. This retrospective study conducted in 2006 describes the impact of philosophical exemption legislation in Arkansas. Methods Arkansas Division of Health data on immunization exemptions granted were linked to Department of Education data for all school attendees (grades K through 12) during 2 school years before the legislation (2001–2002 and 2002–2003 Years 1 and 2, respectively) and 2 years after philosophical exemptions were available (2003–2004 and 2004–2005 Years 3 and 4, respectively). Changes in numbers, types, and geographic distribution of exemptions granted are described. Results The total number of exemptions granted increased by 23% (529 to 651) from Year 1 to 2; by 17% (total 764) from Year 2 to 3 after philosophical exemptions were allowed; and by another 50% from Year 3 to 4 (total 1145). Nonmedical exemptions accounted for 79% of exemptions granted in Years 1 and 2, 92% in Year 3, and 95% in Year 4. Importantly, nonmedical exemptions clustered geographically, suggesting concentrated risks for vaccine-preventable diseases in Arkansas communities. Conclusions Legislation allowing philosophical exemptions from school immunization requirements was linked to increased numbers of parents claiming nonmedical exemptions, potentially causing an increase in risk for vaccine-preventable diseases. Continued education and dialogue are needed to explore the balance between individual rights and the public’s health.