Objective. To study neurophysiological characteristics of persistent idiopathic facial pain (PIFP) in comparison to trigeminal neuralgia. Material and methods. Forty-five patients with PIFP at the age from 25 to 74 years (42 women and 3 men), 25 patients with trigeminal neuralgia at the age from 25 to 84 (15 women and 10 men) and 20 healthy volunteers were examined. Multimodal evoked potentials (EP): brainstem auditory (BAEPs), trigeminal (TEPs) and sympathetic skin responses (SSRs) evoked potentials were recorded. EEG with functional tests (hyperventilation, rhythmical photic stimulation and test with eye opening) was recorded as well. Results. The neurophysiological pattern of PIFP includes: 1) shortening of the latent period (LP) and an increase in peak amplitudes of short-latent components of the BAEPs on both sides in combination with signs of brainstem structure dysfunction (fusion of II—III or III—IV peaks, bifurcation of peaks and lengthening of inter-peaks intervals); 2) normal parameters of the TEPs; 3) an increase in the amplitude of autonomic components (sympathetic and parasympathetic without signs of predominance of the tone of this or that system), intensification of the autonomic reaction; 4) disorganization and acuity of the alpha rhythm, smoothing of zonal differences, presence of bilateral tapering alpha-, theta- or alpha-theta waves on the EEG. Conclusion. Patients with PIFP have significant changes in EP and EEG connected with brainstem structure dysfunction and irritation of subcortical structures and autonomic disorders.