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Stunting in Indonesia was higher and still a serious problem in poor rural areas. The aims of the current study were to assess the prevalence of and risk factors associated with stunting among children aged 6 to 59 months in rural areas of Yogyakarta province of Indonesia. The study based on case control design. The cases were stunted children and controls were the children without stunting from October to December 2018. Data was collected by interviewing children mothers and measured length or height of 23 children as cases and 91 children as controls. Logistic regression analysis was performed to identify the best model of factors leading of stunting in rural area. Odds ratio and 95% confidence interval were used as a measure of association. The mean age of the children was 30,3 and standard deviation was 16,08 months, and 65 (57%) are males. Twenty three (20,2%) children were stunted. Of the stunted children, eight (34,8%) were severely stunted. Education of mother (OR was 5,23, 95% CI 1,97 to 13,90), diarrhea (OR was 6,67, 95% CI 2,37 to 18,73), acute respiratory infection (OR was 9,95, 95% CI 3,54 to 27,95) were factors of stunted children. Acute respiratory infection was found significantly as determinant factors of stunted children in rural area (OR was 9,95, 95% CI 3,54 to 27,95). Understanding of the risk factors for stunting among children aged less than five years in rural area is important to guide Indonesian government public health planners to develop nutrition programs and interventions for stunting.