Background: The stringent recognition requirement between microRNA (miRNA) and its target site suggests that naturally occurring polymorphisms in miRNA target sites might have significant functional implications for miRNA binding and post-transcriptional regulation and consequently affect susceptibility of chronic obstructive pulmonary disease (COPD). Methods: To investigate the influence of putative polymorphisms in miRNAs target sites on COPD, we searched out polymorphisms in miRNA target sites through bioinformatics analysis and conducted a case-control study including 286 patients and 287 healthy controls. Results: Among the 392 polymorphisms of miRNA target sites examined, we found that 5 polymorphisms (GTF3C5 rs7324G＞ A, NUCB1 rs1058491G＞A, C16orf55 rs17177787C＞G, ARHGEF15 rs3744649G＞T, and PTST1 rs3757417 T＞G) had a significant effect on the risk of COPD. In silico analysis revealed that the rs7324 on GTF3C5, rs1058491 on NUCB1, rs3757417 on TPST1, rs17177787 on C16orf55 and rs3744649 on ARHGEF15 were targeted by miR-1469, miR-492, let-7i, has-miR-7-1 and miR-197, respectively. Conclusion: Our findings provide the first evidence that polymorphisms in miRNA target sites could affect susceptibility to COPD.