Background: Gut microbiota is a diverse group of bacteria living in digestive tract of human. Imbalance of this community (dysbiosis) was linked to several gastrointestinal diseases. Our objective was to assess the alterations in gut microbiota among patients with colorectal disorders. Methodology: This study enrolled 70 patients with colorectal diseases and 30 controls. All participants were subjected to total colonoscopy and biopsy taking for histopathology investigation. Stool samples were collected, homogenized and divided to four portions for aerobic, anaerobic culture and 16S rRNA PCR based sequencing analysis. Results: This study included 30 patients with ulcerative colitis (UC), 20 patients with colorectal adenoma (CRA) and 20 patients with colorectal carcinoma (CRC). Regarding microbiota analysis in controls, Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes represented 72.7%, 15.1%, 9.1% and 3.0% respectively. None of the potential pathogens H. pylori and Pseudomonas spp. were isolated. For UC patients, Firmicutes, Proteobacteria and Actinobacteria represented 51.4%, 32.4% and 14.3% respectively. None of Bifidobacterium spp. was isolated from UC patients. For CRA and CRC patients, Proteobacteria was the most frequently isolated (38.7%, 56.7%) followed by Firmicutes (29.0%, 17.8%) and then the Bacteroidetes (20.9%, 13.4%) respectively. Isolated H. pylori and Pseudomonas spp. represented (9.6% &16.4%) and (8.1% & 14.9%) from CRA and CRC patients respectively. The totally isolated Firmicutes in controls, UC, CRA and CRC patients were 24, 3.6, 1.4 and 2 times the isolated Bacteroidetes respectively. Conclusion: Gut microbiota differs between patients and controls. Future studies can assess modifying gut microbiota in high-risk CRC patients as a preventative intervention.