The clinical benefit of early magnetic resonance imaging (MRI) in severe and moderate head injury is unclear. We sought to explore the prognostic value of the depth of lesions depicted with early MRI, and also to describe the prevalence and impact of traumatic brainstem lesions. In a cohort of 159 consecutive patients with moderate to severe head injury (age 5-65 years and surviving the acute phase) admitted to a regional level 1 trauma center, 106 (67%) were examined with MRI within 4 weeks post-injury. Depth of lesions in MRI was categorized as: hemisphere level, central level, and brainstem injury (BSI). The outcome measure was Glasgow Outcome Scale Extended (GOSE) 12 months post-injury. Forty-six percent of patients with severe injuries and 14% of patients with moderate injuries had BSI. In severe head injury, central or brainstem lesions in MRI, together with higher Rotterdam CT score, pupillary dilation, and secondary adverse events were significantly associated with a worse outcome in age-adjusted analyses. Bilateral BSI was strongly associated with a poor outcome in severe injury, with positive and negative predictive values of 0.86 and 0.88, respectively. In moderate injury, only age was significantly associated with outcome in multivariable analyses. Limitations of the current study include lack of blinded outcome evaluations and insufficient statistical power to assess the added prognostic value of MRI when combined with clinical information. We conclude that in patients with severe head injury surviving the acute phase, depth of lesion on the MRI was associated with outcome, and in particular, bilateral brainstem injury was strongly associated with poor outcomes. In moderate head injury, surprisingly, there was no association between MRI findings and outcome when using the GOSE score as outcome measure.