Question Transcranial direct current stimulation (tDCS) is a non-invasive brain stimulation technique that modulates cortical excitability and activity in a polarity-dependent way. In the human motor system, such cortical modulations are inferred through changes in the amplitude of motor evoked potentials (MEPs). To directly evaluate tDCS-induced changes at the cortical level, we investigated polarity-dependent tDCS-induced effects on the motor system, evaluating changes in MEPs, TMS-evoked potentials (TEPs) and in the EEG oscillatory activity. Methods Sixteen young healthy right-handed subjects participated in this study. Two experimental sessions were performed for each subject in randomized order: anodal and cathodal tDCS (a- and c-tDCS). The EEG activity was recorded from 10 scalp electrodes while EMG activity was recorded from the right FDI. Corticospinal excitability and cortical reactivity were investigated through the recording of MEPs and TEPs, whereas the cortical state was evaluated through the acquisition of the EEG activity. All the measures were collected before tDCS, immediately and 30 min after tDCS, to evaluate short and long-lasting tDCS effects. The tDCS was applied for 13 min (1 mA) over the left primary motor cortex. The TEP-MEP block consisted of 100 TMS pulses (intensity of 110% of the RMT), delivered with a random inter stimulus interval of 2–4 s. The EEG block consisted of 3 min of recording during a resting state. To determine the tDCS induced changes in the cortical evoked potentials, a local mean field power analysis was computed. To characterize tDCS-induced changes in cortical oscillatory activity, the EEG power density was estimated by means of the Fast Fourier transform. Results The application of a- and c-tDCS over M1 induced respectively a short-term increase and decrease of MEPs amplitude. The MEPs changes persisted 30 min after a-tDCS but not after c-tDCS. The TEPs analysis highlighted short term changes induced by tDCS polarities. Particularly, we found a significant pattern of topographically specific and current-dependent changes. a- and c-tDCS induced consistent differences in cortical reactivity only on the stimulated area. The long lasting changes partially overlapped those observed in the short-term analyses. Finally, the EEG frequency analysis revealed a significant main effect only in the theta and alpha bands, suggesting a general increase in their power density after tDCS. These changes were reduced 30 min after stimulation. Conclusions a-tDCS over primary motor cortex induced an enhancement of corticospinal excitability, whereas c-tDCS produced an excitability reduction. More interestingly, the cortical reactivity resulted increased after anodal stimulation whereas cathodal stimulation produced a decrease over the stimulated area. These cortical reactivity changes lasted for at least30 min. Moreover, a general increase in the power density of theta and alpha frequencies was also present over all scalp sites for both the stimulation polarities. These results shows direct evidence that tDCS induces polarity-dependent changes on brain activity at cortical level.