The development of distant metastases is the final stage in the progression of solid cancer and is responsible for the majority of cancer-related deaths. Epithelial-mesenchymal transition (EMT) is involved in cancer progression and metastasis. In the present study we used different types of intracellular bacteria isolated from colorectal cancer biopsies to examine their effect on the expression of SNAI1 and VIM genes in Caco2 cell line. SNAI1 gene expression was significantly decreased after cocultivation of Caco2 cells with Pseudomonas aeruginosa, Proteus vulgaris, Proteus mirabilis, Enterococcus faecalis, Klebsiella pneumoniae and Bacillus cereus, respectively (P<0.05). We observed more than 2-fold increase in VIM gene expression within Caco2 cells after cocultivation with Proteus vulgaris. On the other hand, VIM gene expression decreased by half after cocultivation with Pseudomonas aeruginosa and Proteus mirabilis (P<0.05). Our data suggest bacteria presented in colorectal carcinoma tissues may cause changes in gene expression of EMT-associated genes. Further research is needed to find out whether bacteria are capable to support EMT and cancer progression.