Background: It has been suggested that intestinal microbiota of allergic and non-allergic children differs in composition, and that microbiota-immune system interactions may predispose children to develop sensitization. Previous studies have examined fecal microbiota of allergic children with atopic dermatitis, but little is known about that of atopic wheezy children. Objective: To investigate the composition of the fecal microbiota of young sensitized wheezy and non-sensitized non-wheezy children, using molecular methods. Methods: Within the context of a prospective birth cohort, we carried out a nested case-control study of sensitized wheezy children (cases) and non-sensitized non-wheezy controls. Cases and controls were matched for age, sex, parental atopy, allergen exposure, and pet ownership. We evaluated the composition of fecal microbiota by nucleic acid-based methods (PCR combined with denaturing gradient gel electrophoresis and quantification of bifidobacteria by fluorescent in situ hybridization). Results: Thirty-three case-control pairs (mean age 4.4 years) provided stool samples. Comparison of total bacterial community profiles showed that each child had a unique fecal microbiota (mean Dice's similarity coefficient 22%, range 3.3-60.8%). There was no difference between the groups in prevalence of Lactic Acid bacteria (12/33 vs. 11/33, P = 0.8) or bifidobacteria (30/33 vs. 31/33, P = 1.00, cases vs. controls). The bifidobacterial species detected were similar in both groups. The percentage of bifidobacteria in total fecal microflora was no different between cases (median 1.7%, range 0-20.8%) and controls (1.9%, 0-18.2%, P = 0.7). However, cases with eczema had significantly fewer bifidobacteria (median 1.6%, range 0-4.8%) than their controls (4.0%, 1.9-18.2%, P = 0.05). Conclusion: We found no differences in fecal microbiota composition between sensitized wheezy and non-sensitized, non-wheezy children aged 3-5 years using nucleic acid-based methods. Differences appear to be isolated to those allergic children with eczema. © 2005 Blackwell Publishing Ltd atopic.