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To gain insight into the neurophysiological mechanisms involved in Zen meditation, we evaluated the effects of focused attention (FA) on breathing movements in the lower abdomen (Tanden) in novices. We investigated hemodynamic changes in the prefrontal cortex (PFC), an attention-related brain region, using 24-channel near-infrared spectroscopy during a 20-minute session of FA on Tanden breathing in 15 healthy volunteers. We found that the level of oxygenated hemoglobin in the anterior PFC was significantly increased during FA on Tanden breathing, accompanied by a reduction in feelings of negative mood compared to before the meditation session. Electroencephalography (EEG) revealed increased alpha band activity and decreased theta band activity during and after FA on 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 FA on Tanden breathing.