Neurochemical mechanisms mediating the interaction between emotional and cognitive processing are not yet fully understood. Here, we utilized acute tryptophan depletion (ATD) to reduce the brain synthesis of serotonin (5-HT), which is thought to have a central role in regulation of emotions and mood in humans. ATD effects on event-related potentials and magnetic fields were studied using a passive odd-ball paradigm in a randomized, double-blinded, controlled, cross-over design. Auditory responses were recorded simultaneously with high-resolution magnetoencephalography (MEG) and electroencephalography (EEG) in 14 healthy subjects, 5 h after ATD or a control condition. ATD significantly increased depressed mood and lowered plasma tryptophan concentration (total tryptophan decreased by 75%, free tryptophan decreased by 39%). As compared with the control condition, ATD increased the amplitudes of mismatch negativity (MMN) to duration and frequency changes and decreased the latencies of magnetic MMN to frequency changes in the hemisphere ipsilateral to the ear stimulated. Further, ATD modulated N1m latencies and decreased P2m source activity. ATD increased the interhemispheric latency difference of MMNm to frequency changes. No effects on P50 were observed. The present results suggest serotonergic modulation of preattentive auditory change detection, suggested to initiate involuntary attention shifting in the human brain.