In the absence of "hard" neurophysiologic markers, the burden of proof for establishing conscious awareness in individuals who sustain severe brain injury lies in behavioral assessment. Because behavior represents indirect evidence of consciousness, reliance on behavioral markers presents significant challenges and may lead to misdiagnosis. Detection of conscious awareness is confounded by numerous factors including fluctuations in arousal level, difficulty differentiating reflexive or involuntary movement from intentional behavior, underlying sensory and motor impairments, and medication side effects. When an ambiguous behavior is observed, the onus falls to the clinician to determine where along the continuum of unconsciousness to consciousness, it lies. This paper (1) summarizes the current diagnostic criteria for coma, the vegetative state, and the minimally conscious state, (2) describes current behavioral assessment methods, (3) discusses the limitations of behavioral assessment techniques, (4) reviews recent applications of functional neuroimaging in the assessment of patients with disorders of consciousness, and (5) concludes with a case study that illustrates the disparity between behavioral and functional neuroimaging findings that may be encountered in this population.