As an essential repressor, the homeobox gene Hesx1/HESX1 is required within the anterior neural plate for normal forebrain development. Mutations within the Hesx1 gene have been associated with GH deficiency or combined pituitary hormone deficiency. We detected the polymorphism of Hesx1 gene by PCR-SSCP and DNA sequencing methods in 702 individuals from four Chinese cattle breeds. A novel single nucleotide polymorphism (SNP) (IVS1 + 382T > C) was detected. The frequencies of genotype TC in four breeds were 0.000-0.222. Polymorphism of the Hesx1 gene was shown to be associated with growth in the Nanyang breed. Individuals with genotype TC was significantly lower average daily gain than TT at 18 months (P < 0.05).