Introduction: The aim was to compare event-related potentials and event-related de/synchronisations between the P300 and mismatch negativity paradigms, both recorded in the subcortical structures and thus illustrate conscious cognition process in these structures. The second aim was to uncover if the mismatch negativity can be found in subcortical structures. Methods: We included patients with Parkinson's disease, generalised dystonia, essential tremor and epilepsy in the deep brain stimulation program. The electrodes were implanted into the subthalamic nucleus, internal globus pallidus, then in the anterior and ventral intermediate nucleus of the thalamus bilaterally. We were interested in local oscillations. Results: We found a significant P300 - mismatch negativity difference at 250-400 ms latency in the basal ganglia and thalamus in event-related potentials in 7 out of 8 patients. There was also a significant difference in eventrelated de/synchronisations at 500-1500 ms latency in 7 out of 8 patients in the beta band and desynchronisation in the subthalamic nucleus plus the internal globus pallidus and synchronisation in the anterior thalamic nucleus. When the mismatch negativity protocol was processed we found a significant outcome in event-related potentials (100-250 ms latency) in the internal globus pallidus and the ventral intermediate nucleus of the thalamus in 4 out of 6 patients. Conclusion: The results suggest that the subthalamic nucleus, internal globus pallidus and maybe also the thalamus are involved firstly in the subconscious cognitive process 100-250 ms after the stimuli, then in the conscious cognitive processes at the level of the afferent information processing network at 250-400 ms and finally they affect conscious cognitive activity at a time of large brain neuronal network 500-1500 ms after stimuli.