Motivated by increasing religious intolerance, we study the socio-economic covariates of individual-level religious intolerance in Indonesia, the largest Muslim democracy in the world. We use panel data from 2007 and 2014 of more than 20,000 adult individuals (representing 83% of the population) and apply fixed-effect regression analysis to identify relevant socio-economic characteristics that are highly associated with religious intolerance at the individual level. We utilize survey questions on willingness to accept someone with different faith living in the same village, living in the same neighborhood, renting a house, marrying relatives or children, and building a place of worship in the neighborhood as our measures of religious intolerance. We find that higher individual income and educational attainment are positively correlated with the tolerance level. At the same time, a higher level of self-declared religiosity is negatively correlated with a tolerant attitude. For location-specific characteristics, higher income inequality and extent of poverty in the location where an individual resides are associated with a higher level of religious intolerance. These patterns are generally robust across different measures of religious intolerance, although there is heterogeneity in the magnitudes of the correlations, where these covariates have the smallest correlations with the willingness to accept interfaith marriage in the family.