VRTNgenes play an important role in the early development of the thoracic of the embryo, and regulate the number and development of the thoracic vertebrae. To investigate the association between single nucleotide polymorphisms（SNP） of the VRTN gene and the thoracic vertebrae number in Kazakh sheep, we utilized the PCR-SSCP technique to examine the polymorphism of the VRTN gene in a sample of 399 Kazakh sheep. The correlation between the VRTN gene of Kazakh sheep and the quantitative traits of thoracic vertebrae was analyzed by independent chi-square test, and the results of PCR-SSCP experiment were confirmed by DNA sequencing technology. We discovered a significant association between the SNP（rs82505838: C＞T） in Kazakh sheep and the thoracic vertebrae number（P＜0.01）, which notably deviated from the Hardy-Weinberg equilibrium. The results indicated that the VRTN gene SNP（rs82505838: C＞T） could influence the thoracic vertebrae count in Kazakh sheep and could serve as a marker for this trait and a molecular marker for future genetic breeding efforts in Kazakh sheep.