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Abstract Background The Composite Index of Anthropometric Failure (CIAF) can comprehensively identify undernutrition by combining several indicators of nutritional status – namely, weight-for-age, length/height-for-age and weight-for-length/height – to determine the nutritional status of children under five years of age. This study aims to assess undernutrition using the CIAF and its determinants on children under five years of age in the Bogor District, Indonesia. Methods A cross-sectional study was conducted during February–May 2019 among 330 mother-children pairs (with children under five), selected by systematic random sampling from four villages as undernutrition pockets in the rural area of Bogor District, Indonesia. The nutritional status of the children was assessed by measuring weight and length/height. Z-score was calculated using WHO Anthro software and was categorized based on conventional indices, including weight-for-age (WAZ), length/height-for-age (HAZ) and weight-for-length/height (WHZ). The CIAF is measured based on a combination of conventional index measurements. In addition, mothers’ and childrens’ characteristics and clean living behaviour are assessed via structured questionnaires. Environmental sanitation is assessed using the environment meter. Binary logistic regression analysis with SPSS version 22.0 is used to analyse the dominant factors associated with undernutrition. Results Among children under five, 42.1% experienced anthropometric failure (overall prevalence of undernutrition based on the CIAF), 2.4% experienced wasting only, 5.8% were classified as both wasting and underweight, 2.1% as wasting, underweight and stunting, 16.4% as underweight and stunting, 11.5% as stunting only, and 3.9% as underweight only. Assessment of nutritional status using a conventional anthropometric index shows that respective prevalences of underweight, stunted and wasted were 27.8, 29.7, and 10.6%. The mother’s height is the most dominant factor associated with anthropometric failure [p = 0.008; AOR = 1.95; 95% CI: 2.19–3.19]. The most dominant factors associated with the conventional undernutrition indices of underweight, stunted and wasted are, respectively, family income [p = 0.018; AOR = 5.44; 95% CI: 1.34–22.11], mother’s height [p = |