Background Children unreached by vaccination are at higher risk of poor health outcomes and India accounts for nearly a quarter of unvaccinated children worldwide. The objective of this study was to investigate compositional and contextual determinants of non-receipt of childhood vaccines in India using multilevel modelling. Methods and Findings We studied characteristics of unvaccinated children using the District Level Health and Facility Survey 3, a nationally representative probability sample containing 65 617 children aged 12-23 months from 34 Indian states and territories. We developed four-level Bayesian binomial regression models to examine the determinants of non-vaccination. The analysis considered two outcomes: completely unvaccinated (CUV) children who had not received any of the eight vaccine doses recommended by India's Universal Immunization Programme, and children who had not received any dose from routine immunisation services (no RI). The no RI category includes CUV children and those who received only polio doses administered via mass campaigns. Overall, 4.83% (95% CI: 4.62-5.06) of children were CUV while 12.01% (11.68-12.35) had received no RI. Individual compositional factors strongly associated with CUV were: non-receipt of tetanus immunisation for mothers during pregnancy (OR = 3.65 [95% CrI: 3.30-4.02]), poorest household wealth index (OR = 2.44 [1.81-3.22] no maternal schooling (OR = 2.43 [1.41-4.05]) and no paternal schooling (OR = 1.83 [1.30-2.48]). In rural settings, the influence of maternal illiteracy disappeared whereas the role of household wealth index was reinforced. Factors associated with no RI were similar to those for CUV, but effect sizes for individual compositional factors were generally larger. Low maternal education was the strongest risk factor associated with no RI in all models. All multilevel models found significant variability at community, district, and state levels net of compositional factors. Conclusion Non-vaccination in India is strongly related to compositional characteristics and is geographically distinct. Tailored strategies are required to overcome current barriers to immunisation.