This study aimed to identify the factors that affect the incidence rate of neglected children in Indonesia by considering the household effect. Neglect is a form of child abuse by not fulfilling or ignoring their basic needs. Neglected children are a complex social problem. This is a multidimensional problem, since the cause cannot be seen only based on individual characteristics, but it must also consider the household variation effect. The data was collected from a secondary source, namely the Socio-Culture and Education Module of the 2012 National Socio-Economic Survey (NSES-SCEM) that consisted of 75,000 households' data. The response variable was the child status of neglect, while the explanatory variables included a child's background characteristics at individual and household level. Two-level binary logistic regression with a random effect was applied. The regression model results show that neglected children were more commonly boys, had one or both parents dead, were younger in age, have another neglected child in the households, have disabilities, live in an uninhabitable house, headed by young and/or lower educated adults, had lower economic status, have higher underage family members, had unemployed parents, and lived with one of her/his parents. The current study found that the individual and household level remains an important aspect of child neglect in Indonesia. Policies in Indonesia should be directed to improve household welfare and to create a specific intervention to identify and assist vulnerable children in society.