Most studies have shown that MMP2 and TIMP2 are involved in the development of colon cancer; however, due to the fact that CNIs affect morphology of many organs, the main goal of this study was to analyze the morphology of the rat’s jejunum after long-term treatment with calcineurin inhibitor-based immunosuppressive drugs and to investigate their impact on the location of MMP-2 and its inhibitor TIMP-2, as well as the balance between them. Here, TIMP2 is linked to malignant colon neoplasm.