Purpose The objectives of this study were, firstly, to determine the diversity of the host's gut microbiota in irritable bowel syndrome (IBS) using a culture-independent method (DGGE of the 16S rRNA gene) and, secondly, to examine mucosal biopsies of IBS patients and compare them to their own fecal microbiota. Methods The diversity of the dominant microbiota in the fecal material of IBS patients was compared to a healthy control group. In addition, we compared the mucosal and fecal microbiota of IBS patients. Results Statistical analysis of the mean similarity data for these groups indicated a significant difference (P < 0.001) between IBS (n=47) and healthy controls (n=33) with significantly more variation in the gut microbiota of healthy volunteers than that of IBS patients. The average intra-individual similarity between the mucosa and luminal microbiota was 84\%, which indicates that different communities were present at the two sites. This difference, however, is similar to that previously described between these two niches in control subjects. The average inter-individual similarity of the bacterial communities on the mucosa and in the lumen of IBS was not significantly different (P > 0.05). Conclusions IBS impacts equally on both bacterial communities in the IBS host and a significant difference in the gut microbiota exists between fecal samples from IBS patients and healthy controls. The reason for this difference is unclear and various possible explanations are available, but much more work is required to determine the underlying reason for this observation.