The role of brain biopsy is well established in patients with neoplastic lesions, with a diagnostic yield approaching 95%. The diagnostic yield of brain biopsy in adults with neurological decline varies from 20% to 43%. Only a few studies have examined the diagnostic yield of brain biopsy in children with idiopathic neurological decline. A retrospective analysis was conducted on all open and closed pediatric brain biopsies performed between January 1988 and May 2003. Biopsies were performed for diagnostic purposes in patients showing a progressively deteriorating neurologic course in whom less-invasive modalities such as neuroimaging, electroencephalography (EEG), and molecular genetic studies were either negative or inconclusive. Immunocompromised patients were included. Patients were excluded if the preoperative diagnosis was a neoplasm or if the patient was undergoing a resection as part of a work-up for intractable epilepsy. Each patient underwent numerous investigations before brain biopsy. The utility of each biopsy was analyzed. Sixty-six children had brain biopsies performed for diagnostic purposes during the study period. Patient ages ranged from 2 months to 16 years and 9 months at the time of biopsy. The diagnostic yield was 48.5% overall, with a yield of 68.8% between 1996 and 2003. Of the total, 26 (39.4%) biopsies were both diagnostic and useful. Patients most frequently presented with seizures (56.1%) and encephalopathy (33%). The most frequently diagnosed disease was vasculitis (18.2%). A total of 71.9% of patients with diagnostic biopsies improved with appropriate treatment. Brain biopsy in children had a diagnostic yield of 48.5% in our series. A specific diagnosis may help in management and outcome, especially with a diagnosis of vasculitis.