The effects of histone deacetylase (HDAC) inhibitors on epithelial-mesenchymal transition (EMT) differ in various cancers. E‑cadherin is a cell‑to‑cell adhesion protein, whereas accumulation of vimentin is related to the development of the spindle shape of the mesenchymal cell phenotype. We investigated the EMT phenotypes of human cholangiocellular carcinoma HuCC‑T1, JCK and SNU‑1079 cell lines. To this end, we measured the expression of E‑cadherin or zonula occludens (ZO)‑1 and vimentin, epithelial and mesenchymal cell markers, respectively, using real‑time reverse transcription‑polymerase chain reaction, western blotting, and immunofluorescence microscopy following treatment with trichostatin A (TSA, 200 nM) or valproic acid (VPA, 0.5 mM) with or without gemcitabine (GEM, 50 nM) for 24 h. In addition, we performed cell morphology, migration, and invasion assays. HuCC‑T1 cells changed from spindle‑ to rectangular‑shaped after co‑treatment with GEM and TSA or VPA. Furthermore, cells co‑treated with GEM and TSA or VPA exhibited protein levels of E‑cadherin or ZO‑1 that were higher than those in cells treated with GEM alone, indicating stronger inhibition of EMT. However, vimentin expression was also increased. Confocal microscopy revealed enhanced expression of E‑cadherin or ZO‑1 and vimentin in all three cell lines. Migration and invasion were inhibited in HuCC‑T1 cells co‑treated with GEM and TSA or VPA, compared to those treated with GEM alone. In conclusion, co‑treatment of cholangiocarcinoma cells with TSA or VPA and GEM suppressed EMT with tolerable cytotoxicity. However, the HDAC inhibitors augmented both E‑cadherin and vimentin expression and their effects varied in different cholangiocarcinoma cell lines. Therefore, the clinical use of HDAC inhibitors in biliary cancer should be considered cautiously.