Abstract： Objective To investigate the effects of S100A6 gene on invasion of human pancreatic cancer cell and possible mechanism. Methods Human pancreatic cancer BxPC3 cell line was transfected with small interfering RNA (siRNA) targeting S1006 gene, the mRNA and protein levels of S100A6 were determined by real time RT-PCR and Western blotting respectively. The invasion ability was evaluated by Transwell chamber. The matrix metalloproteinase-2 (MMP-9) activity of cancer cells was examined by gelatin zymography. Results The levels of mRNA and protein of S100A6 were greatly reduced in a dose and time dependent manner, the number of penetrating cells was greatly reduced in a dose dependent manner. The expression of S100A6 mRNA in 12.5 nmol/L of S100A6 siRNA transfected group decreased from ( 100 ±0.3)％ in control group to (15.3 ±0.2)％ ; while the expression of S100A6 protein decreased from (83.2 ±0. 18 ) ％ to ( 13.5 ± 0. 12) ％ ; the number of penetrating cells decreased from 44.5 ± 2.2 to 7.6 + 1.5 ( P ＜0. 01 ). The MMP-9 activity of siRNA group reduced significantly. Conclusions S100A6 siRNA can inhibit the invasion of pancreatic cancer cells through down-regulation of MMP-9.