Schizophrenia is one of the most debilitating diseases among psychiatric disorders. Recent studies suggest the existence of effective immunological changes in the pathophysiology of this disease. The purpose of the current study was to determine the changes in serum levels of Brain Derived Neurotrophic Factor (BDNF) and Nerve Growth Factor-beta (NGF) in schizophrenic patients before treatment and 40 days after treatment. In this case-control study, serum levels of BDNF and NGF were measured by ELISA in 26 patients with schizophrenia and 26 healthy controls. All patients were treated with clozapine or risperidone for 40 days. A positive and negative syndrome scale (PANSS) questionnaire has been used to recognize the severity of the disease and to assess the response to treatment. Neurotrophin concentrations were compared before and after the treatment and with control groups using paired t-test and ANOVA test. BDNF and NGF levels in the case group were more than levels after treatment, but these differences were significant only for NGF. Concentrations in both neurotrophins were higher than the control group. The statistically significant difference was observed between changes in the NGF levels in the case and the control group, while no significant difference was seen in changes of BDNF. The main conclusion to be drawn from this study was that the increase in BDNF and particularly NGF may have an important role in causing schizophrenia. And possibly drugs clozapine and risperidone help to treat the disease by reducing the concentration of Neurotrophins.