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Objective: To investigate the effect of knockdown of EpCAM by siRNA on invasion, migration, and colony abilities in hypopharyngeal carcinoma FaDu cells., Methods: A siRNA against EpCAM was employed to inhibit the expression of EpCAM in FaDu cells. Measurements included the Transwell assay for invasion and migration, plate colony formation assay for cell colony ability, Western blot assay for EpCAM, E-cadherin, and β-catenin expressions in total protein, cytoplasm, and cytoskeleton, respectively., Results: mRNA and protein expressions of EpCAM were suppressed significantly in FaDu cells transfected by EpCAM siRNA (t = 6.46, P < 0.05; t = 10.25, P < 0.05) . Transwell assay showed in transwell assay, the average invasive cells in EpCAM siRNA cells (26.33 ± 3.71) was less than that in FaDu cells (61.47 ± 6.70; t = 7.95, P < 0.05)and control cells (54.13 ± 6.51; t = 6.42, P < 0.05); the average number of migration cells in EpCAM siRNA cells (79.87 ± 8.44) was lower than that in FaDu (167.53 ± 11.49; t = 10.90, P < 0.05) cells and control cells (162.13 ± 13.45; t = 8.97, P < 0.05). In plate colony formation assay, the average colony number of EpCAM siRNA cells was (78.00 ± 5.57), which was less than that of FaDu cells(177.30 ± 16.50; t = 9.78, P < 0.05) and control cells (173.67 ± 13.50; t = 11.35, P < 0.05). Western blot assays showed, silencing of EpCAM increased the expressions of E-cadherin (t = 4.58, P = 0.01) and β-catenin (t = 3.76, P = 0.02) in cytoskeleton, and decreased the expressions of E-cadherin (t = 6.60, P < 0.05) and β-catenin (t = 8.20, P < 0.05) in cytoplasm., Conclusions: The knockdown of EpCAM inhibits the invasion, migration, and colony formation abilities of FaDu cells, which is probably related to the regulation of E-cadherin and β-catenin in cytoplasm and cytoskeleton, and EpCAM may be a promising gene therapy target for hypopharyngeal carcinoma.