In humans, hyperventilation (HV) has various effects on systemic physiology and, in particular, on neuronal excitability and synaptic transmission. However, it is far from clear how the effects of HV are mediated at the cortical level. In this study we investigated the effects of HV-induced hypocapnia on primary motor (M1) and visual cortex (V1) excitability. We used: (1) motor and phosphene threshold (MT / PT) and (2) stimulus-response (S-R) curves (i.e. recruitment curves) as measures of excitability. In the motor cortex, we additionally investigated (3) the intrinsic inhibitory and facilitatory neuronal circuits using a short-interval paired pulse paradigm. Measurements were performed before, during and after 10 min of HV (resulting in a minimum end-tidal pCO₂ of 15 mm Hg). HV significantly increased MEP amplitudes, particularly at lower TMS intensities. Paired-pulse stimulation indicated that HV decreases intracortical inhibition (ICI) without changing intracortical facilitation (ICF). The results suggest that low pCO₂ levels modulate, in particular, the intrinsic neuronal circuits of ICI, which are largely mediated by neurons containing -aminobutyric acid (GABA). Modulation of MT probably resulted from alterations of Na⁺ channel conductances. A significant decrease of PT, together with higher intensity of phosphenes at low stimulus intensities, furthermore suggested that HV acts on the excitability of M1 and V1 in a comparable fashion. This finding implies that HV also affects other brain structures besides the corticospinal motor system. The further exploration of these physiological mechanisms may contribute to the understanding of the various HV-related clinical phenomenona.