Objectives Despite the adoption of WHO’s Expanded Programme on Immunisation in Indonesia since 1977, a large proportion of children are still completely unimmunised or only partly immunised. This study aimed to assess factors associated with low immunisation coverage of children in Indonesia.

Setting Children aged 12–59 months in Indonesia.

Participant The socioeconomic characteristics and immunisation status of the children were obtained from the most recent Demographic and Health Survey, the 2012 Indonesia Demographic and Health Survey. Participants were randomly selected through a two-stage stratified sampling design. Data from 14 401 children aged 12–59 months nested within 1832 census blocks were included in the analysis. Multilevel logistic regression models were constructed to account for hierarchical structure of the data.

Results The mean age of the children was 30 months and they were equally divided by sex. According to the analysis, 32% of the children were fully immunised in 2012. Coverage was significantly lower among children who lived in Maluku and Papua region (adjusted OR: 1.94; 95% CI 1.42 to 2.64), were 36–47 months old (1.39; 1.20 to 1.60), had higher birth order (1.68; 1.28 to 2.19), had greater family size (1.47; 1.11 to 1.93), whose mother had no education (2.13; 1.22 to 3.72) and from the poorest households (1.58; 1.26 to 1.99). The likelihood of being unimmunised was also higher among children without health insurance (1.16; 1.04 to 1.30) and those who received no antenatal (3.28; 2.09 to 5.15) and postnatal care (1.50; 1.34 to 1.69).

Conclusions Socioeconomic factors were strongly associated with the likelihood of being unimmunised in Indonesia. Unimmunised children were geographically clustered and lived among the most deprived population. To achieve WHO target of protective coverage, public health interventions must be designed to meet the needs of these high-risk groups.