Aim: The etiology of schizophrenia has been linked to complex interactions of genetic and environmental factors, and among them are genes that regulate BDNF (Brain-derived Neurotrophic Factor) expression. The BDNF has been linked to the pathophysiology of schizophrenia, particularly the Val66Met polymorphism. This study aims to assess BDNF Val66Met polymorphism and its role in positive and negative symptoms in patients with schizophrenia in East Java. Subjects and Methods: A total of 52 subjects with schizophrenia living in East Java were assessed for BDNF Val66Met polymorphism. The analysis was performed using Statistical the Social Sciences (SPSS) software version 22. Clinical assessment was conducted using the positive and negative syndrome scale (PANSS). Data were analyzed using linear regression multivariate analysis. Results: Our study found that Val/Met polymorphism is associated negatively with the total PANSS scores (beta coefficient = -12.299, p = 0.017). The Val/Val polymorphism is associated with negative symptoms (beta coefficient = 22.607, p = 0.043). The present study’s findings considered age, gender, education level, number of antipsychotics consumed, medication adherence, and duration of untreated psychosis. Conclusion: Val/Val polymorphism is associated with a higher PANSS total score. Val/Met genotype is associated with more severe positive symptoms, while the Val/Val genotype is associated with more negative symptoms. Further study with a larger and multicenter sample is needed to clarify further the relationship of BDNF polymorphism to clinical outcomes of schizophrenia.