Evaluation of the physical fitness level of children and adolescents must include consideration of individual growth rates. This study evaluates the relationship between height and physical fitness in a large sample of 6-17 yr students. Physical fitness test scores were calculated for every 1 cm height group and used to generate quadratic regression equations. Physical fitness data reported by the Ministry of Education, Culture, Sports, Science and Technology in Japan (MEXT) were compared with estimated values obtained using our regression equations. The differences between the values reported by MEXT and our estimated values were very small. Comparison of physical fitness T-scores calculated based on school grade averages with T-scores based on means calculated using our regression equations indicated that shorter height students had lower T-scores if school grade averages were used for the calculation. In conclusion, in elementary and junior high school students, it is important to evaluate physical fitness level relative to individual physical growth.