This study aims at an application of rough set theory to illustrate the relationship between human psychological and physiological states. Recent behavioral medicine studies have revealed that various human secretory substances change according to mental states. These substances, the hormones and immune substances, show temporal increase against mental stress. Thus, it is frequently introduced as biomarkers of mental stress. The relationship between these biomarkers and human chronic stress or daily mental states was also suggested in the previous studies. However the results of these studies were inconsistent. Some technical reasons were indicated for this discrepancy. Among that, we focused on the analysis technique investigating the relationship between human psychological state, i.e., scores of a psychological scale, and physiological state, i.e., level of the secretory biomarkers. In this paper, we introduced Rough Set analysis method instead of using a conventional linear correlation analysis method. In the experiment, the salivary secretory immunoglobulin A (IgA), which is a major stress biomarker, of 20 male students was assessed before and after a short-term stressful mental workload. Also, 65 items of psychological mood scale was assessed as a psychological index. The result showed that some items strongly related with the change in the IgA, while no significant linear correlation among that was obtained.