Minerals play important roles in biological processes. Hair mineral analysis has the advantages of conveniences in sampling and observing the profiles of multiple minerals simultaneously. The purpose of this study was to compare hair mineral contents between urban and local middle school students, and to find out the relation with nutrient intakes and clinical symptoms. Ten nutritional minerals and 7 environmental mineral contents were analyzed in the hair samples of 44 and 37 male students who resided in urban and local area, respectively. And their nutrient intake and clinical symptom score were estimated from questionnaire. The average age, height, and weight were 15.1 years, 168.4 cm, 56.8 kg in urban subjects and 15.4 years, 169.1 cm, 61.9 kg in local subjects, respectively. The residence types were apartment (63.6%) and small-sized apartment (22.7%) in urban subjects and apartment (51.4%) and house (37.8%) in local subjects. The primary water sources were purified water (38.3%), running water (18.2%) in urban subjects and purified water (32.4%), underground water (27.0%) in local subjects, respectively. Daily energy and nutrient intakes were not significantly different between two groups. Among the surveyed 17 clinical symptoms, the scores of constipation, cold, anxieties and total score of clinical symptoms in urban subjects were significantly love. than those in local subjects. Hair contents of Na, Mg, Ca, Cu, V Al, As were significantly higher, while U was lower in urban subjects compared to those in rural subjects. Hair contents of Ni and U were significantly correlated with food intake, and Cr, V, Al, Sb, As, U showed a correlation with energy intake. Hair Mg level showed significantly negative correlation with total clinical symptom score. In conclusion, hair mineral profile between urban and local students was significantly different. And some of these minerals were significantly correlated with food and nutrient intakes. Especially hair magnesium was significantly correlated with total clinical symptom score. Therefore, hair mineral levels would be needed for more systematic study elucidating potentiality as a useful clinical tool.