Variants of the BTB/POZ domain-containing protein 9 gene (BTBD9) (rs4714156, rs9357271, and rs9296249) and the serotonin 5-HT-2C receptor gene (HTR2C) (rs518147 and rs3813929) were reported to be associated with Tourette syndrome (TS) in White population recently. To examine the association between variants of the BTBD9 and the HTR2C genes and patients with TS among a Chinese Han population, 110 patients with TS and 440 sex-matched, age-matched, and ethnicity-matched healthy controls underwent sequencing and association analysis. There was a statistically significant association between the variant rs9296249 of the BTBD9 gene and the TS phenotype. However, no statistically significant associations were found between the other four variants (rs4714156, rs9357271, rs518147, and rs3813929) and the TS phenotype (P>0.05). Larger-scale studies are warranted to further define the relationship between variant rs9296249 of the BTBD9 gene and the risk of developing TS.