The case of stunting in Indonesia was higher and still becomes an important issue in poor rural areas. Research objective is to examine the prevalence rate and associated factors with stunting in children aged 6-59 months in rural areas of Bantul, Yogyakarta, Indonesia. This study applied a case-control design. The cases group were stunted children and the control group was not stunted children from October to December 2018. The data was collected by interviewing selected mothers of 6-59 months children and measuring the length/height of 23 children as a case group and 91 children as a control group. Research location used two rural areas in Bantul Yogyakarta. This study used logistic regression analysis to identify the best model of factors leading to stunting in rural areas. Analysis to measure of association used 95% CIs and "Adjusted" ORs. The prevalence of stunting was 20.8% out of which 52.2% were mild, 4.3% were moderate and 43.5% were severe. The mean of children age in the case and control group were 31.78 16.8 and 29.92 15.96 months with the mean of height for age Z score were-3.23 1.03 and-0.14 1.22 respectively. Diarrhea was found significantly as the determinant factor of stunted children in rural areas (AOR=7.79, 95% CI 2.59-23.33, p = 0.001). The results showed diarrhea as determinants factor of stunting in children under five in rural areas, it is important to assist the Indonesian government to develop a program to address the problem of stunting associated with the environment
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