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ABSTRACT: To study the association between the single nucleotide polymorphisms (SNPs) in FXYD6 gene and schizophrenia in a family-trios population. Six SNPs (rs10790212, rs11544201, rs555577, rs1815774, rs4938446 and rs497768) in the FXYD6 gene were genotyped by allele-specific PCR method in 101 nuclear families, and transmission disequilibrium test (TDT) was performed. SNPs rs10790212 and rs11544201 showed significant association with schizophrenia (P<0.05). Furthermore, significant association of schizophrenia with the haplotype rs10790212-rs11544201 was found (P<0.05). FXYD6 gene might play an important role in schizophrenia susceptibility and functional analysis of FXYD6 are needed.