Introduction: The gut microbiome acts as a real organism and many changes in its composition have been reported in colorectal cancer (CRC). Short-chain fatty acids (SCFA) mainly produced as microbial metabolites, acetate, propionate, and butyrate acids. In this study, we investigate the relation between the microbiome structure and the level of SCFA in patients with CRC compared to non-CRC. Methods: The study consists of fourteen subjects with CRC and 14 non-CRC were included in this casecontrol study. Stool sample were analysed for SCFA (acetate, propionate and butyrate acids) with gas chromatography and an exploration of the diversity bacteria was undertaken using 16S rRNA gene denaturing gradient gel electrophoresis (DDGE). Results: Analysis of PCR-DGGE from CRC were showed dissappearance of Bifidobacterium compared non-CRC.Concentrations of acetate, propionate and butyrate acids had lower siginificantly with mean 8.55 μg/mL, propionate 5,61 μg/mL and butyrate acids 3,79 μg/mL respectively. Conclusion: Nowdays, microbome has shown its important role for human either for disease and health, as we know that SCFA is the main products of anaerobics microbial fermentation in the large intestine and affect colonic health. In study, all patients with colorectal cancer were showed disappearance of dominant band from Bifidobacterium groups.The study suggest that there is a different spectrum of the Bifidobacterium from CRC and non-CRC patients. In CRC patients we found lower SCFA concentrate than non-CRC.