While computed tomography (CT) is the appropriate technique for the urgent detection of hematomas and contusions in the cerebral hemispheres, it is much less effective at documenting diffuse injury and posterior fossa lesions, and is therefore only partially predictive of outcome. More recently, magnetic resonance imaging (MRI) has been used, particularly to examine posterior fossa structures, but the relationship between brainstem injury and outcome is unclear and the types of brainstem injury are poorly understood. The aim of this study was to use acute MRI to examine the types of brainstem injury following severe traumatic brain injury (TBI) and their relationship to supratentorial injury. We also aimed to correlate these findings with outcome at 6 months (Glasgow Outcome Scale [GOS] score). Forty-six patients (mean age, 34 years, range, 16-70 years; 76% male) admitted to a regional neurocritical care unit with TBI requiring ventilation underwent CT and MRI (T2, FLAIR, gradient echo) scanning within 3 days (median, 1 day) of injury. GOS was ascertained by outpatient interview. Brainstem lesions were detected in 13 patients by MRI, only two of which were detected by CT. Eleven out of 13 patients with brainstem injury had an unfavorable outcome (death, vegetative state, or severe disability), of whom five died. Of the 33 patients without brainstem lesions, 18 had an unfavorable outcome, of whom four died. The direct relationship between brainstem lesions and unfavorable outcome was statistically significant (p < 0.05, chi-squared test). With regard to supratentorial injury, all but two brainstem lesions were seen either in the context of severe diffuse axonal injury or a significant mass lesion, and all of these patients had a poor outcome. However, the two patients with brainstem injury and good outcome had relatively few supratentorial abnormalities. From these observations, we have devised a simple classification system that is useful clinically and has potential associations with outcome. Poor prognosis is common following major TBI but is more common in those with brainstem injury. However, brainstem injury is not an absolute indicator of poor outcome. Understanding the anatomy and extent of brainstem injury, as well as its relationship to supratentorial abnormalities, will facilitate a more accurate use of early MRI as a prognostic tool and assist in the counseling of families.