Background and aims A general dysbiosis of the intestinal microbiota has been established in patients with Crohn's disease (CD), but a systematic characterisation of this dysbiosis is lacking. Therefore the composition of the predominant faecal microbiota of patients with CD was studied in comparison with the predominant composition in unaffected controls. Whether dysbiosis is present in relatives of patients CD was also examined. Methods Focusing on families with at least three members affected with CD, faecal samples of 68 patients with CD, 84 of their unaffected relatives and 55 matched controls were subjected to community fingerprinting of the predominant microbiota using denaturing gradient gel electrophoresis (DGGE). To analyse the DGGE profiles, BioNumerics software and non-parametric statistical analyses (SPSS V. 17.0) were used. Observed differences in the predominant microbiota were subsequently confirmed and quantified with real-time PCR. Results Five bacterial species characterised dysbiosis in CD, namely a decrease in Dialister invisus (p = 0.04), an uncharacterised species of Clostridium cluster XIVa (p = 0.03), Faecalibacterium prausnitzii (p