Persistent vegetative state (PVS, apallic syndrome) has become a significant medical and social problem. The outcome of young people with PVS is a matter of great interest. Therefore, we analysed the outcome of 127 children and adolescents who were in PVS for at least 30 days following traumatic (n = 82) or hypoxic (n = 45) brain injury. After 19 months of follow-up, 84% of the patients of the traumatic brain injury (TBI) group, but only 55% of the hypoxic brain injury (HBI) group had left PVS (p < 0.001). The TBI patients regained consciousness earlier. Later than 9 months post trauma less than 5% of the patients of both groups left PVS. Hypoxic brain injury patients had a higher incidence of seizures (p = 0.01) and a higher seizure frequency. They had significantly more complications like pneumonia, gastrointestinal disturbance or myositis ossificans (= heterotopic ossification). Posttraumatic hyperthermia and autonomic dysfunctions were correlated with worse outcome in the TBI group, but not in the HBI group. Thirteen patients (16%) with TBI became independent in everyday life versus only two (4%) with HBI. These results underline the important contribution of hypoxia in severe and permanent brain impairment. They also may help to establish the prognosis of children in PVS.