To evaluate trends in rates of personal belief exemptions (PBEs) to immunization requirements for private kindergartens in California that practice alternative educational methods. We used California Department of Public Health data on kindergarten PBE rates from 2000 to 2014 to compare annual average increases in PBE rates between schools. Alternative schools had an average PBE rate of 8.7%, compared with 2.1% among public schools. Waldorf schools had the highest average PBE rate of 45.1%, which was 19 times higher than in public schools (incidence rate ratio = 19.1; 95% confidence interval = 16.4, 22.2). Montessori and holistic schools had the highest average annual increases in PBE rates, slightly higher than Waldorf schools (Montessori: 8.8%; holistic: 7.1%; Waldorf: 3.6%). Waldorf schools had exceptionally high average PBE rates, and Montessori and holistic schools had higher annual increases in PBE rates. Children in these schools may be at higher risk for spreading vaccine-preventable diseases if trends are not reversed.