[Purpose] The aim of this study was to investigate the effects of balneotherapy on immunological parameters, trace metal elements and mood states in pilots. [Subjects] Thirty-six healthy male pilots were enrolled into this study. [Methods] All subjects received therapy for 3 weeks. They took entire-body immersion baths in thermomineral water for 30 min a day for 3 weeks. Blood samples were taken 1 day before and after the balneotherapy treatment. Blood concentrations of trace metal elements were measured using a BH5100 atomic absorption spectrometer. Blood serum concentrations of immunoglobulins and complements were measured with an automatic biochemical analyzer. The Profile of Mood States test was conducted to determine changes in mood states. [Results] After 3 weeks of balneotherapy, the concentrations of immunoglobulin A and complement component 4 increased significantly and the blood concentration of lead significantly decreased. The mood scores of tension-anxiety, anger-hostility, fatigue-inertia and confusion-bewilderment decreased. The mood score of vigor-activity significantly rose. [Conclusion] The findings indicate that balneotherapy over a 3-week period may exert a beneficial influence on the immune system and play an assistive role in improving the mood states of pilots.