BACKGROUND AND AIMS: Perturbations in the intestinal microbiota composition, as a result of changed lifestyles, may be involved in the development of atopic diseases. We examined the gut microbiota composition in early infancy and the subsequent development of atopic manifestations and sensitisation. PATIENTS AND METHODS: Faeces of 957 one-month-old infants, participating in the KOALA Birth Cohort Study, were analyzed using quantitative real-time PCR. Information on the manifestation of atopic symptoms (eczema, wheeze) and potential confounders was retrieved through repeated questionnaires. Total and specific IgE were measured in venous blood samples collected during home visits at the infant's age of 2 years. During these home visits also a clinical diagnosis of atopic dermatitis was made according to the UK Working- Party criteria. RESULTS: The presence of E. coli was associated with a higher risk of developing eczema (ORadjusted = 1.87; 95%CI 1.15-3.04), this risk being increased with increasing numbers of E. coli (Pfor trend = 0.016). Infants colonised with C. difficile were at higher risk of developing eczema (ORadjusted = 1.40; 95%CI 1.02- 1.91), recurrent wheeze (ORadjusted = 1.73; 95%CI 1.08- 2.77) and allergic sensitisation (ORadjusted = 1.54; 95% CI 1.02-2.31). Furthermore, the presence of C. difficile was also associated with a higher risk of a diagnosis of atopic dermatitis during the home visit (ORadjusted = 1.73; 95%CI 1.08-2.78). CONCLUSION: This study demonstrates that differences in the gut microbiota composition precede the manifestation of atopy. Since E. coli was only associated with eczema, whereas C. difficile was associated with all atopic outcomes, the underlying mechanims explaining these association may be different.