This study was conducted to investigate the differences in food habits, eating behaviors and food frequency by gender and regions in upper grade elementary school children in Korea. Subjects of this study were 1,211 children, 645 boys and 566 girls, attending 6 elementary schools (4th, 5th and 6th graders). 389 children lived in Seoul and 822 children lived in other regions. Mean height, weight and BMI of subjects were 142.4 cm, 38.7 kg and 18.8 kg/m2 respectively. 70.5% of the subjects had breakfast every day and 12.4% of the subjects skipped breakfast. There were significant differences between boys and girls in causes of skipping breakfast, overeating, meal volume, and duration of meals. Girls showed more desirable eating behavior than boys (p < 0.001). Scores for specific eating behaviors such as unbalanced diet and intake of meats and vegetables were better in girls (p < 0.001), and boys ate meals faster than girls (p > 0.001). There were significant differences between Seoul and other regions in eating behavior. Eating behavior scores of children in other regions were higher than in Seoul (p < 0.01). Children in Seoul had a higher frequency of watching television with meals. Frequency of fruits (p < 0.001), milk products (p < 0.01), and meats (p < 0.05) of children in Seoul were higher than other regions. Otherwise the frequency of simple sugar products of children in other regions was higher than Seoul (p < 0.001). Frequency of green vegetables was higher for girls than boys, and frequency of fast foods was higher for boys than girls. These results showed that in nutrition education programs designed to improve the nutritional health of elementary school children, we need to focus more on differences in the children's food habits and eating behaviors by gender and regions. In consideration of these differences, such educational programs need to have a different emphasis for each gender and regions to serve its specific needs.