Inspiratory loading in awake humans is associated with electroencephalographic signs of supplementary motor area (SMA) activation. To provide evidence for a functional connection between SMA and the diaphragm representation in the primary motor cortex (M1_DIA), we tested the hypothesis that modulating SMA activity using repetitive transcranial magnetic stimulation (rTMS) would alter M1_DIA excitability. Amplitude and latency of diaphragm motor evoked potentials (MEPDIA), evoked through single pulse M1_DIA stimulation, before and up to 16 minutes after SMA stimulation, were taken as indicators of M1_DIA excitability. MEPs from the first dorsal interosseous muscle (FDI, MEP_FDI) served as a control. Four SMA conditioning sessions were performed in random order at one-week intervals. Two aimed at increasing SMA activity (5Hz and 10Hz, both at 110% of FDI active motor threshold). Two aimed at decreasing it (1Hz either at 110% of FDI active or resting motor threshold, referred to as aMT or rMT). 5Hz increased MEP_DIA and MEP_FDI amplitudes with a maximum 11-16 min. post stimulation (p=0.04 and p=0.02 respectively). 10Hz increased MEP_FDI amplitude with a similar time course (p=0.03), but did not increase MEP_DIA amplitude (p=0.32). Both aMT and rMT failed to decrease MEP_DIA or MEP_FDI amplitudes (p=0.23 and p=0.90, respectively, for diaphragm and p=0.48 and p=0.14 for FDI). MEP_DIA and MEP_FDI latencies were unaffected by rTMS. These results demonstrate that 5 Hz rTMS over the SMA can increase the excitability of M1_DIA. These observations are consistent with the hypothesis of a functional connection between SMA and M1_DIA.