Gilles de la Tourette syndrome (GTS) is a neurodevelopmental disorder characterized by motor and vocal tics. The etiology of the disorder is unknown, although the predominant role of genetic factors has been established. Variants of the BTBD9 gene (rs4714156, rs9296249 and rs9357271) have been reported to be associated with GTS in French Canadian and Chinese Han populations. Therefore, we decided to test the association between GTS and polymorphisms of the BTBD9 gene in Polish patients. Our cohort of GTS cases comprised 162 patients aged 4-54 years (mean age: 19.9 ± 8.7 years; 131 males, 80.9 percent). The control group consisted of 180 healthy persons aged 14-55 years (mean age: 23.1 ± 2.1 years; 149 males, 82.8 percent). The rs4714156, rs9296249 and rs9357271 variants of the BTBD9 gene were genotyped. No significant differences were found in minor allele frequencies (MAFs) of the SNPs tested between the two groups. The frequency of MAFs of the genotyped SNPs was lower in GTS patients with Attention Deficit Hyperactivity Disorder (for rs9357271 and rs9296249, P=0.039 and rs4714156, P=0.040) and higher in GTS patients without comorbidities (for rs9357271 and rs9296249 P=0.021 and rs4714156 P=0.025). There was a trend toward an association between the minor allele of the SNPs and mild tics (P=0.089 for rs9357271 and rs9296249, P=0.057 for rs4714156). Despite limitations of the study, including the small number of cases and analyzed SNPs, our results suggest that the examined BTBD9 variants are not associated with GTS risk, but may be associated with comorbidity and tic severity in the Polish population.