OBJECTIVES: The first objective of this study was to compare the presence of specific peptides that can be found in the stool of patients diagnosed with inflammatory bowel disease (IBD) (ulcerative colitis, UC and Crohn's disease, CD) with the stool of a healthy person. The second objective was to examine whether there are differences in the presence of certain peptides in the stool sample of a UC patient compared to the stool sample of a CD patient and whether that would help in differentiation UC from CD. STUDY DESIGN: The study was done as a cross-sectional study. PARTICIPANTS AND METHODS: Ten stool samples from patients diagnosed with CD, ten stool samples from patients diagnosed with UC and ten stool samples from healthy controls (K) were analyzed. Samples were prepared by extraction in water, re-extraction in an organic solvent, evaporation and desalting using the ZipTip method according to the manufacturer's instructions. The prepared samples were analyzed on a MALDI-TOF mass spectrometer Bruker UltrafleXtreme (Bruker Daltonics, Bremen, Germany) in the range of 1000-4000 m/z in positive reflectron mode with HCCA as matrix. RESULTS: In tested samples we have searched for specific peptides: peptides specific for control samples, peptides specific for control samples and samples of IBD patients, the most significant diagnostic peptides for IBD, peptides specific for UC, peptides specific for CD and the total peptides that can be found in IBD patients. Statistically significant differences were found for all groups of characteristic peptides when samples from control group and samples from IBD patients (UC and CD) were compared. Statistically significant differences between UC and CD samples were found for peptides specific for CD. CONCLUSION: There is a significant difference in the presence of specific peptides in the stool of patients diagnosed with IBD in regard to the stool of a healthy person. Sufficient levels of difference in specific peptide frequency which would allow practical differentiation of UC and CD samples have not been found because in our research small number of specific CD peptides were found in control samples too.