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Identifying risk factors of incomplete immunization among children is crucial to developing relevant policies to improve immunization coverage. In this study, we investigated factors associated with incomplete immunization among children in Indonesia and elucidated differences in risk factors between urban and rural areas. The data came from a national-wide survey, the 2017 Indonesia Demographic Health Surveys. In total, 3264 children aged 12–23 months were included in the study. An incomplete immunization status was defined as a child who did not complete the ten doses of basic vaccinations, consisting of one dose of bacille Calmette-Guérin, one dose of hepatitis B, three doses of pentavalent vaccine (diphtheria, pertussis, tetanus, hemophilus influenza type B, and hepatitis B vaccine), four doses of polio vaccine, and one dose of measles vaccine. Generalized linear mixed models were constructed to examine the effects of different levels of risk factors on the incomplete immunization status. We further conducted stratified analyses by urban and rural areas. About 40% of the 3264 children were incompletely immunized, among whom 45.3% were in urban areas and 54.7% were in rural areas. Eight of the 34 provinces had incomplete immunization rates exceeding 50%, and the Papua and Maluku regions had the highest rates of incomplete child immunization. The multivariate analyses showed that when women attended fewer than four antenatal care sessions and resided outside the Nusa Tenggara region, their children were more likely to have incomplete immunization in both urban and rural areas. On the other hand, having no health insurance was positively associated with incomplete immunization in urban areas, whereas having received a tetanus vaccination during pregnancy was negatively associated with incomplete immunization in rural areas. Results of this study suggest that tailored interventions should be developed to address significant risk factors in rural and urban areas. [ABSTRACT FROM AUTHOR]