Polymorphisms in the vitamin D receptor (VDR) gene are associated with idiopathic short stature (ISS) in several countries. This study aimed to identify a possible correlation between polymorphisms in the VDR promoter in Chinese children with ISS and the efficacy of the recombinant human growth hormone (rhGH) treatment. Pre-pubertal children with ISS and healthy age- and gender-matched children (N = 95 each) were enrolled in this study. Two single nucleotide polymorphisms (SNPs) in the VDR promoter (rs11568820 at the Cdx-2-binding site upstream of exon 1e and rs4516035 at -1012 upstream of exon 1a) were typed. The growth velocity, standard deviation score (SDS) of height for chronological age, height SDS for bone age, predicted adult height, and serum insulin-like growth factor 1 (IGF-1) and IGF-binding protein 3 (IGFBP-3) levels of the ISS patients were determined before and 6 months after rhGH treatment. No significant differences were observed in the genotype frequencies between the ISS cases and controls. After rhGH treatment, the growth velocity of the A/G genotype at the Cdx-2-binding site SNP locus was significantly higher than that of the G/G genotype; the IGF-1 and IGFBP-3 levels were also higher in the treated group than the untreated group. However, these changes were independent of the VDR-promoter genotype. Polymorphisms in the VDR promoter may not result in the pathogenesis of ISS in Chinese children. The A/G genotype showed a significantly higher growth velocity than the G/G genotype, and may represent a short-term marker of growth potential.