The relative abundance of different groups of sulphate reducing bacteria (SRB) in faecal DNA collected before and after therapy from patients suffering with Crohn's disease (CD), irritable bowel syndrome (IBS) or ulcerative colitis (UC) has been compared with that from healthy controls. Growth tests revealed that SRB were not more abundant in samples from CD patients before treatment than in the healthy control group. For most of the 128 samples available, these preliminary results were confirmed using degenerate PCR primers that amplify the dsrAB gene. However, some samples from CD patients before treatment contained a growth inhibitor that was absent from IBS or UC samples. In-depth sequencing of PCR-generated dsrB fragments revealed that the diversity detected was surprisingly low, with only 8 strains of SRB and the sulphite reducing bacterium, Bilophila wadsworthia, detected above the 0.1% threshold. The proportion of the two major species detected, B. wadsworthia and Desulfovibrio piger, was as high as 93.5% of the total SRB population in the healthy control group, and lower in all patient groups. Four previously undescribed species were found: it is impossible to predict whether they are sulphate or sulphite reducing bacteria. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.