Discrepancies often exist between recorded immunization coverage and the real immunity level in a community. To estimate the vaccination coverage against measles in south-east Islamic Republic of Iran, a cross-sectional study was conducted in 3 districts during summer 2011. Using probability proportional to size cluster sampling, 1368 children aged 30–54 months were selected. Serum samples of 663 who had received 2 injections of mumps-measles-rubella (MMR) vaccine were checked for anti-measles IgG. Vaccination coverage for the second dose of MMR vaccine was 93.7%. The prevalence of anti-measles IgG in those who had received at least 2 MMR vaccine doses was 94.6%. There was a statistically significant association between the serological results and variables that reflected poor accessibility to health services. Combining serological results with coverage data, the proportion of the community protected against measles was estimated as 88.6%, which was below the limits defined for the measles elimination goals.