One hertz transcranial magnetic stimulation (TMS) over the motor cortex has been reported to increase activity in the motor cortex contralateral to stimulation, as evidenced by the elevated motor evoked potential on the corresponding hand muscle. Little research, however, has assessed concomitant changes in the haemoglobin level in the unstimulated motor cortex. An aim of this study was to measure the change of oxy- and deoxy-haemoglobin levels in the left motor cortex after 20 min of 1 Hz TMS over the right motor cortex. Subjects carried out a finger to thumb tapping task sequentially with six blocks of ten cycles (30 s on and 60 s off). One block was performed before TMS and five after TMS. The results show that the level of oxyhaemoglobin in the unstimulated cortex increased after TMS over the contralateral hemisphere and that the increase lasted 40 min after 1 Hz stimulation. Deoxy-haemoglobin was slightly decreased during the first 15 min after stimulation. The results identify long term physiological changes resulting from 1 Hz stimulation and help to inform our understanding of interhemispheric interactions in TMS studies.