We investigated the distribution of short chain fatty acids (SCFA) in enema samples taken from subjects before sigmoidoscopy as an indicator of possible microbial community differences between subjects subsequently diagnosed as normal or having colonic disorders. The major SCFA in all groups were acetic, propionic, and butyric acids. A significantly higher ratio of acetate to total SCFA and lower ratio of butyrate to total SCFA was found for polyp-colon cancer subjects than for normal subjects. There were no significant differences in the ratios of acetate, propionate, or butyrate between the diverticulosis or inflammatory bowel groups and the normal group. There were no significant sex differences nor were there correlations with the ratios of acetate, propionate or butyrate and age, subject weight, or dry weights of samples. Significant differences in concentrations of individual acids were found between normal and certain diagnostic groups. The difference in proportions of individual SCFA between groups suggest differences in fermentation patterns of the colonic microflora.