Discrimination between patients in vegetative (VS) and minimally conscious state (MCS) is currently based upon the behavioral gold standard. Behavioral assessment remains equivocal and difficult to interpret as evidence for the presence or absence of consciousness, resulting in possible clinical misdiagnosis in such patients. Application of an operational architectonics (OA) strategy to electroencephalogram (EEG) analysis reveals that absence of consciousness in patients in VS is paralleled by significant impairment in overall EEG operational architecture compared to patients in MCS: neuronal assemblies become smaller, their life span shortened, and they became highly unstable and functionally disconnected (desynchronized). However, in a previous study, patients with different brain damage etiologies were intermixed. Therefore, the goal of the present study was to investigate whether the application of OA methodology to EEG could reliably dissociate patients in VS and MCS independent of brain damage etiology. We conclude that the observed EEG OA structure impairment in patients in VS and partial preservation in patients in MCS is a marker of consciousness/unconsciousness rather than physiological damage. Results of this study may have neuroscientific, clinical, and ethical implications.