The conflict between vergence (eye movement) and accommodation (crystalline lens deformation) occurs in every stereoscopic display. It could cause important stress outside the "zone of comfort", when stereoscopic effect is too strong. This conflict has already been studied using questionnaires, during viewing sessions of several minutes. The present pilot study describes an experimental protocol which compares two different comfort conditions using electroencephalography (EEG) over short viewing sequences. Analyses showed significant differences both in event-related potentials (ERP) and in frequency bands power. An uncomfortable stereoscopy correlates with a weaker negative component and a delayed positive component in ERP. It also induces a power decrease in the alpha band and increases in theta and beta bands. With fast responses to stimuli, EEG is likely to enable the conception of adaptive systems, which could tune the stereoscopic experience according to each viewer.