The micro-flora of the proximal jejunum in healthy volunteers was compared with the micro-flora in patients with gastrointestinal symptoms suggestive of spontaneous bacterial overgrowth in the small intestine. Biopsies were taken distally to the ligament of Treitz with a Watson capsule. The samples were diluted and inoculated on selective and non-selective agar plates that were incubated aerobically and anaerobically. No major differences were found in the small jejunum micro-flora in healthy persons or in a heterogenous group of patients with gastrointestinal disorders. Oropharyngeal micro-organisms dominated the micro-flora in all subjects and colonic micro-organisms were found in low numbers in a few subjects from both groups. Streptococcus intermedius and Haemophilus parahaemolyticus were only found in the micro-flora of healthy subjects while Lactobacillus spp. was more frequently found in the samples from patients. Eight of 20 healthy subjects and five of 18 patients met the criterion of small intestinal overgrowth. Emerging evidence suggests that other factors are involved in the pathogenesis of the irritable bowel syndrome complex. There is a need for better understanding of the complicated interactions between the host and the endogenous micro-flora.