- Recent years have seen a global trend of declining immunization rates of recommended vaccines that is more pronounced among school-age children. Ethnic disparities in child immunization rates have been reported in several countries. We investigated an effect of ethnicity on the vaccination rates of immunizations routinely administered within schools in Israel. Data were collected from the Ministry of Health database regarding immunization coverage for all registered Israeli schools (3736) in the years 2009-2011. Negative binomial regression was used to assess the association between school ethnicity and immunization coverage while controlling for school characteristics. The lowest immunization coverage was found in Bedouin schools (median values of 75.1%, 81.5% and 0% for the first, second and eighth grades, respectively) in 2011. During this year, vaccination coverage in the first and second grades in Jewish schools was 1.51 and 1.35 times higher, respectively, compared to Bedouin schools. In the years 2009 and 2010, no significant increase in risk for lower vaccination rate was observed in Bedouin schools, and children in Arab and Druze schools were more likely to have been vaccinated. The lower vaccination refusal rate found in Bedouin schools supports the hypothesis that difficulties related to accessibility constitute the main problem rather than noncompliance with the recommended vaccination protocol for school-age children, featuring higher socio-economic status groups. Our study emphasizes the importance of identifying, beyond the national-level data, subpopulation groups at risk for non-vaccination. This knowledge is essential to administrative-level policy-makers for the allocation of resources and the planning of intervention programs.