To gain insight into the neurophysiological mechanisms involved in Zen meditation, we evaluated the effects of abdominal (Tanden) breathing in novices. We investigated hemodynamic changes in the prefrontal cortex (PFC), an ttention-related brain region, using 24-channel near-infrared spectroscopy during a 20-munite session of Tanden breathing in 15 healthy volunteers. We found that the level of oxygenated hemoglobin in the anterior PFC was significantly increased during Tanden breathing, accompanied by a reduction in feeling of negative mood compared to before the meditation session. Electroencephalography (EEG) revealed increased alpha band activity and decreased theta band activity during Tanden breathing. EEG changes were correlated with a significant increase in whole blood serotonin (5-HT) levels. These results suggest that activation of the anterior PFC and 5-HT system may be responsible for the improvement of negative mood and EEG signal changes observed during Tanden breathing.