Confocal laser endomicroscopy (CLE) is a new technique, which allows subsurface histological diagnosis at a cellular and subcellular level in vivo and could provide histological diagnosis during endoscopic examination. Up to now histological examination of the tissue sample is the only definitive way of diagnosis and monitoring organ rejection after transplantation. In case of pancreas transplantation percutaneous pancreas biopsy under imaging control is still the method of choice for obtaining tissue samples. However in 73–89% of biopsy attempts, it was shown that the duodenal histology predicts the initial diagnosis of rejection of the pancreas, usefulness of transplanted duodenum biopsies for graft rejection monitoring was also described. The histology technique is time consuming, and the therapeutic decision could not be made quickly, in spite of clinical necessity. In this paper we described feasibility of visualization and biopsy of donor duodenum and detection of microscopic changes in 2 cases of transplanted duodenum, expressed as destruction of the villi and dispersed goblet cells in comparison to a microscopic view of their own healthy duodenum No or only small, endoscopically non-significant macroscopic changes in transplanted duodenum in those patients were observed. In both cases, the histological examination confirmed acute organ rejection. We demonstrated for the first time that CLE is promising and effective method to detect acute phase of organ rejection and also for follow up in those patients.