Human epithelium was cultured to characterize differences in microbial populations between regions of normal colon and between polyps, inflammatory bowel disease, and cancer and their respective adjacent normal mucosa. Twenty-one patients (12 polyps, 5 inflammatory bowel disease, 4 cancer) underwent colonoscopy with anaerobic culture of mucosal biopsies from normal and diseased ascending, transverse, descending, and sigmoid colon. No differences for total number of organisms and recovery of species between ascending colon and other normal regions were seen except for sigmoid colon. Significant differences between polyps and adjacent normal tissue were seen for total number of organisms and recovery of genera and species. No significant differences in total number of organisms and recovery of genera were seen between cancer and inflammatory bowel disease and their respective adjacent normal tissue. The recovery of genera from polyps and normal tissue was Bacteroides greater than Fusobacterium greater than Clostridium greater than Eubacterium greater than Peptostreptococcus. These data suggest that (i) the total number of anaerobic organisms and species remained relatively constant, except for lower numbers in normal distal colon which were probably a result of the preparation for colonoscopy; (ii) polyp formation favored increased microbial colonization; and (iii) the increased number of organisms generally reflected those genera and species seen on adjacent normal mucosa.