Using functional magnetic resonance imaging (fMRI) or positron emission tomography (PET), much knowledge has been gained in understanding how the brain is activated during controlled experiments of language tasks in alphabetic subjects and in Chinese subjects. While previous studies have compared performance between alphabetic and Chinese subjects, few data were about Japanese-speaking individuals. In this study, we used fMRI to investigate brain activations in processing Japanese phonological and orthographic by visual tasks in six Japanese subjects. Different activation patterns were observed between phonological and orthographic processing. We conclude that constellation of neural substrates was different for phonological processing.