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Computed tomography (CT) is now the primary diagnostic method for head trauma because of its ability to demonstrate the nature, extent, sites, and multiplicity of brain injuries. Although there have been numerous reports on the CT findings of most types of intracranial injury, the findings in brainstem injury have not been well described. This study aimed at comparing the autopsy findings of brainstem in head trauma in comparison with CT scan results. Two hundred patients with head trauma, who expired after a period of time of hospitalization, were assessed in a diagnostic value study. Brain stem involvement was determined by autopsy as well as CT scanning of the brain during their hospitalization. The results of the two methods were compared with each other, emphasizing on the type and location of probable lesions in the brain stem. Considering the autopsy as the method of the choice, sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of CT scan in brain stem lesions of patients with head trauma were calculated. The effect of primary cause of head trauma, survival time and Glasgow Coma Scale (GCS) were evaluated, as well. Brain stem lesions were detected in 39 (19.5%) patients in autopsy. However, CT scan revealed brain stem lesions in 23(11.5%) cases. The sensitivity, specificity, PPV and NPV of CT scan was 59%, 100%, 100% and 91% respectively. The most common lesions of the brain stem region were as contusion of pons (8.5%), medulla (5%) and midbrain (4.5%). There were 6 (3%) cases of ponto-medullary junction tearing and 1 (0.5%) case of cervico-medullary junction tearing. CT scan is a specific method of evaluating patients with probable brain stem injuries after head trauma, but low sensitivity limits its efficacy. Our results are in conformity with the reports in the literature.