With stereoscopic displays, a depth sensation that is too strong could impede visual comfort and result in fatigue or pain. Electroencephalography (EEG) is a technology which records brain activity. We used it to develop a novel brain-computer interface that monitors users' states in order to reduce visual strain. We present the first proof-of-concept system that discriminates comfortable conditions from uncomfortable ones during stereoscopic vision using EEG. It reacts within 1s to depth variations, achieving 63% accuracy on average and 74% when 7 consecutive variations are measured. This study could lead to adaptive systems that automatically suit stereoscopic displays to users and viewing conditions.