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The purpose of this study was to analyze the canonical correlation analysis between physical fitness and body composition and to demonstrate the relation of canonical correlation analysis. The subjects were 323 male and 313 female students of middle school. Body composition was measured by InBody 3.0 of a segmental multifrequency impedance analyzer. The measured items were protein, total body water, fat free mass, fat mass, waist hip ratio, body mass index and basal metabolic rate. The grip strength(left/right), back strength, sit-up, trunk flexion, stand long jump, 50m dash, 1200m/1600m run, stork stand and whole body reaction test in physical fitness were measured. The data were analyzed with simple correlation, multiple correlation and canonical correlation using PC SAS release 8.01. The results were as follow;1. Among factors of physical fitness, strength(left grip) is the most important factor in physical fitness and body composition in the case of male students. 2. Among factors of body composition, fat free mass is the most important factor in physical fitness and body composition in the case of male students. 3. Among factors of physical fitness, strength(left grip) is the most important factor in physical fitness and body composition in the case of female students. 4. Among factors of body composition, protein is the most important factor in physical fitness and body composition in the case of female students.