Objective To investigate the association between the patients with schizophrenia and polymorphism in rs2030324 and rs11030101 of brain derived neurotrophic factor(BDNF).Methods 100 patients with schizophrenia and 100 normal controls were enrolled.The BDNF polymorphism (rs2030324 and rs11030101) and allele frequency were genotyped by sequencing the products of PCR.Genotype and allele frequencies were compared between patients and controls.Symptoms were assessed using the PANSS,and the relationship between the score of PANSS and the polymorphism of rs2030324 and rs11030101 was analyzed.Results There was statistically significance between schizophrenic patients and controls in the distribution of allele frequency in rs2030324(x2 =3.888,P=0.049) and rs11030101 (x2 =5.571,P=0.016).There was statistically significance between schizophrenic patients and controls in the distribution of implicit model in rs11030101 (x2=5.230,P=0.022).The score of PANSS negative symptoms of patients with SNPs rs11030101 different genotypes showed that A/T genotype was the highest(34.60±5.63) and T/T genotype was minimum (28.38±9.96),and the difference had statistical significance (F=4.868,P=0.010).Conclusion The polymorphism in rs2030324 and rs11030101 of BDNF is relate to the patients with schizophrenia among Han Chinese and their allele A increases the risk of illness.The SNP of rs11030101 may be associated with the clinical features of schizophrenia.