The purpose of this study is to develop a T1 mapping method derived from the variable flip angle with an MT pulse. T1 mapping of the brain with an MT pulse was performed in five healthy subjects. The mean T1_MT values were significantly decrease than the T1 in all regions (P < 0.05). The difference of T1 and T1_MT in deep gray matter (included caudate nucleus and putamen) were more decreased than those in white matter. In conclusion, determination of T1 with MT pulse makes it possible to obtain more detailed information of the macromolecular pool and the free water pool.