The treatment of refractory schizophrenia has been a clinical challenge for most psychiatrists; the possible reasons include diagnostic errors,medical conditions and brain dysgenesis.Here,we described a patient with childhood-onset schizophrenia who had severe psychiatric symptoms such as auditory hallucinations and persecutory delusions,and etc.We reexamined all his possible medical conditions and found that the patient had an abnormally enlarged cavus septum pellucidum (CSP) combined with cavum vergae (CV) (maximum length >30 mm).Some reports suggested that abnormal CSP (length >6 mm) has a significant association with schizophrenia.However,abnormally large CSP or CSP/CV and related prognosis were reported rarely.This case suggested that abnormally enlarged CSP or CSP/CV may worsen the prognosis.