Background Inherited factors are involved in the development of chronic obstructive pulmonary disease (COPD). This study was designed to investigate the relationship between polymorphisms of HDEFB1 668 C/G and 1654 G/A loci and susceptibility to COPD in Chinese Han population. Methods After the process of extracting genomic DNA from peripheral blood of COPD smokers and healthy smokers, the loci of genotypes 668 C/G and 1654 G/A were determined by polymerase chain reaction-restriction fragment length polymorphism analysis and polymerase chain reaction-single strand conformation polymorphism analysis. Results With respect to HDEFB1 668 locus, the occurences of CC, CG, GG genotypes were 72.7%, 25.0%, 2.3% in COPD smokers and 53.2%, 38.3%, 8.5% in healthy smokers (P < 0.05, respectively). The allele frequencies of 668 C and 668 G were 85.2% and 14.8% in COPD smokers and 72.3% and 27.7% in healthy smokers ( P < 0.01, respectively, odds ratio was 2.32 with 95% confidence interval 1.37 to 3.72). As to HDEFB1 1654 G/A locus, neither genotype distribution difference nor allele distribution difference was found when comparing COPD smokers with healthy smokers. Conclusion The polymorphism of HDEFB1 668 C/G is associated with susceptibility to COPD in Chinese Han population; furthermore, the 668 G allele represents relatively lower susceptibility to COPD.