The aim of this study was to elucidate the role of CD97 isoforms in gastric carcinoma. Out of four gastric cancer cell lines investigated, BGC-823 cells demonstrating low CD97 protein expression were stably transfected with pcDNA3.1 vector containing CD97/EGF1,2,5 or CD97/EGF1,2,3,4,5 inserts. Behavior of transfected cells was systematically investigated by employing proliferation, motility and invasive assays. As a result, we found that over-expression of CD97/EGF1,2,5 isoform correlated with increased motile and invasive ability of the clones. Furthermore, CD97/EGF1,2,5 isoform over-expression (3.8 times higher) was followed by significant decrease of CD97/EGF1,2,3,4,5 isoform (10.3 times lower). In contrast, CD97/EGF1,2,3,4,5 clones revealed significantly reduced invasive properties as compared with corresponding controls. The changes in acetylation status were one of the possible mechanisms affecting behavior of transfected cells. We concluded from the study that CD97 is closely related with advanced stages and higher invasiveness of gastric carcinoma. The study further lightened the tumor promoting role of CD97 small isoform in cancer progression and indicated the possible suppressive properties of the full length isoform of CD97.