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Children with head trauma are frequently seen in many emergency units. The clinical evaluation of these patients is difficult for a number of reasons and improved diagnostic tools are needed. S-100B, a protein found in glial cells, has previously been shown to be a sensible marker for brain damage after head injury in adults, but few studies have focused on its use in children.In this study, 111 children with head trauma were included and venous blood and urine samples were taken at arrival (S1 and U1) and 6 hours later (S2 and U2). S-100B levels were analyzed. Clinical and radiologic evaluations were performed according to hospital routine. Two groups were identified—group 1: no computed tomography (CT) scan performed or a CT scan without any sign of trauma-related intracranial pathology (n = 105). Group 2: A CT scan with signs of trauma-related intracranial pathology (n = 6).In group 1, the median (inter quartile range) serum S-100B value in S1-samples was 0.111 μg/L (0.086–0.153), and in group 2, it was 0.282 μg/L (0.195–1.44) (p < 0.01). Also, S2 values significantly differed between the two groups. Urine values were, however, not significantly differing between the groups.Serum S-100B values within 6 hours after head trauma in children were significantly higher in patients with intracranial pathology compared with those without intracranial complications. Identification of these high-risk patients already in the emergency department is of major importance, and we suggest that S-100B could be a valuable diagnostic tool in addition to those used in clinical practice today.