Schizophrenia is a severe brain disease seen all over the world. There are studies showing that activator of transcription and developmental regulator AUTS2 (AUTS2) gene is involved in the predisposition to schizophrenia. In this study, we aimed to analyze the correlation between rs6943555 variant of AUTS2 gene and schizophrenia in a Turkish population. This study include 100 schizophrenia patients and 152 unrelated healthy controls. The AUTS2 genotypes were determined by the polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) tests. Chi-square and Anova tests were used for statistical analyses. According to results, although the A allele frequency was higher in schizophrenia patients, we didn't detect statistically significant correlation between schizophrenia and the AUTS2 gene rs6943555 variant (p = 0.057). However after adjusting for gender, significant effects of genotype and allele were detected among males (p = 0.039 and p = 0.049, respectively). Also we observed a statistically significant correlation between HDL cholesterol values of patients and genotypes of rs6943555 variant (p = 0.016). As a result, rs6943555 variant of AUTS2 gene might affect the predisposition to schizophrenia especially in male patients.