Four breeds of chickens (white Leghorn, white recessive rocks, Taihe silkies and Xinhua) with different production performance were applied to screen potential single nucleotide polymorphisms (SNPs) related to production traits in a region of the growth hormone gene using denaturing high performance liquid chromatography (DHPLC). Five SNPs were found in a fragment of 518 bp. In the present study a simple and rapid method to estimate allelic frequencies of SNPs in the case of several SNPs existing in the same targeted DNA fragment was introduced based on the correspondence between the heterozygous DHPLC peak and sequencing genotype, of which the accuracy was evaluated by comparing with the allelic frequencies result of PCR-RFLP. It's a feasible method because no significant difference was detected between the estimated allelic frequencies and those calculated by PCR-RFLP.