BACKGROUND: With the increasing mean height of children, concerns about stature seem to grow in Korea. However, most studies regarding short stature were performed in developing countries where population were likely to be exposed to malnutrition and poor hygienic environments and factors associated with height were seldom studied in well-nourished population. METHODS: Study participants were 449 Korean boys and girls enrolled in 2nd or 6th grade of a primary school. Height and weight were measured by standardized method and a questionnaire asking eating habits, birth weight, feeding method, physical exercise, household income, and height of parents was self-administered to each child and their parents. We classified participants into two groups according to the distribution of their height (lower 25% or upper 75%) and evaluated the factors associated with the short height (lower 25%) using multiple linear logistic regression analysis. RESULTS: In the analysis of the whole participants, short height of parents and normal body mass index were significantly associated with short height. Subgroup analysis stratified by gender and school grade showed that short height of father and normal body mass index, short height of mother, low household income, and not engaging in regular physical exercise were significantly associated with short height for 2nd grade boys, 6th grade boys, 2nd grade girls, and 6th grade girls, respectively. CONCLUSION: The factors associated with short height differed according to gender and school grades. In boys, parental height was significantly associated with and, in girls, environmental factors such as physical exercise or household income were significant factors of short stature.