The purpose of this study is to investigate the relation between the classification ability quotient and cortisol-hormonal change of middle school students. Thirty-three students, second graders in middle school, performed the classification task that can be an indicator of students' classification ability. And then amount of the secreted hormone was analyzed during task performance. The study results were as follows: First, the classification methods of students mostly utilized visual, qualitative. Their classification patterns for each subject were static, partial, and non-comparative. Second, the amount of stress-hormone was secreted from students during the experiment decreased in overall after the free classification. It seemed that student-centered activity relieved stress. Third, the classification ability quotient turned out to be significantly correlated to the stress hormone, which means that there was a close relationship between classification ability and stress level. It was also considered that stress had a positive effect on the improvement of classification ability. This study provided physiologically more accurate information on the stress increased in the learning process than other conventional studies based on reports or interviews. Finally, researchers could recognize the effect of stress in the cognitive activity and the need to find an appropriate level of stress in learning processes.