Background: This study evaluated usefulness of automated databases in identifying vaccine exemptions. It also studied social characteristics and health care utilization patterns of children who were exempted from immunization. Methods: We conducted an observational cohort study of children aged 0 through 6 years enrolled in two large health plans. We used both the immunization registry and medical record to identify the child’s vaccine exemptions and assess the child’s status regarding recommended vaccinations. We categorized children into racial, education, and income groups based on the distribution of these characteristics in his/her community from 2001 census data. We used administrative data to identify the child’s utilization on well-child, outpatient, prescriptions, ER and hospital visits. The knowledge of these characteristics will provide critical information on designing interventions to improve immunization compliance and long-term follow-up with these children. Results: We compared exemption information found in the medical record with that found in the administrative data of our chart review sample. Although negative predictive value of the electronic data compared to the chart reviews was 92% and 90% for 2-year and 6-year olds, respectively, positive predictive value was only 52% and 62%, respectively. Additionally, our results indicate that exemptors are more likely to come from well-educated, higher income areas than non-exemptors. Exemptors were found not to have opted out of the health care system and continue, although less frequently for the age 2 group, to use services in the health plans. Conclusions: Without better-automated data and the need for chart reviews, tracking of children with immunization exemption status would be expensive. Since parents of exemptors are well-educated, interventions should focus on communicating to parents of exemptors the most updated information on vaccines and vaccine preventable diseases.