To study the role of intestinal flora in the pathogenesis of RA, we have applied computerized gas-liquid chromatography (GLC) for bacterial cellular fatty acids (CFAs) present in the stool. The CFA spectra represents the total composition of bacterial CFAs in a faecal sample. Correlation and cluster analysis of CFA spectra gathers samples with quantitatively and qualitatively similar bacterial flora into clusters, which then reveal the relationship of samples to each other. Stool samples were collected at the time of hospital admission from patients with early RA before any specific treatment. The CFA spectra in stool samples of RA patients were significantly different from those of non-RA controls. Patients with erosive RA formed a group most clearly different from the controls. Analyses based on the CFA composition of reference bacteria revealed that anaerobic bacteria are primarily responsible for the differences observed. These results suggest that intestinal bacteria play a role in the development of RA.