Functional near-infrared spectroscopic imaging (NIRS imaging) has the potential to elucidate the relationship between neuronal activity and oxygenation responses. However, its signal specificity to the functional cortex is sometimes spoiled by its rough spatial resolution. In this study we incorporated transcranial magnetic stimulation (TMS) motor mapping into an NIRS imaging study to enhance spatial specificity to the functional cortex. Distinctive biphasic responses in the cortical oxygenation status were observed in the center of the primary motor cortex during a motor task. The early response phase, occurring within 1 to 3 seconds after task initiation, represents a cortical deoxygenation which consists of a significant increase in deoxygenated hemoglobin concentration (HbR) and a nonsignificant decreasing tendency in oxygenated hemoglobin concentration (HbO(2)). The delayed response phase represents an excess of incoming blood flow, which appears as an increase in HbO(2)/total Hb (tHb) and a decrease in HbR following the early response. In the surrounding area, cortical oxygenation change showed a monophasic response consisting of an increase in HbO(2)/tHb and a decrease in HbR. Combining TMS mapping with NIRS imaging enabled us to specify the cortex with the strongest functional activity.