BACKGROUND: Epidemiological studies have suggested that gastro-intestinal infections including Helicobacter pylori, intestinal microflora (commensal bacteria) and geohelminths may influence the risk of asthma and allergy but data from early life are lacking. OBJECTIVE: We aimed to determine the independent effects of these infections on allergic disease symptoms and sensitization in an Ethiopian birth cohort. METHODS: In 2008/09, 878 children (87% of the 1006 original singletons in a population-based birth cohort) were followed up at age 3 and interview data obtained on allergic symptoms and potential confounders. Allergen skin tests to Dermatophagoides pteronyssinus and cockroach were performed, levels of Der p 1 and Bla g 1 in the child's bedding measured and stool samples analysed for geohelminths and, in a random subsample, enterococci, lactobacilli, bifidobacteria and H. pylori antigen. The independent effects of each exposure on wheeze, eczema, hayfever and sensitization were determined using multiple logistic regression. RESULTS: Children were commonly infected with H. pylori (41%; 253/616), enterococci (38.1%; 207/544), lactobacilli (31.1%; 169/544) and bifidobacteria (18.9%; 103/544) whereas geohelminths were only found in 8.5% (75/866). H. pylori infection was associated with a borderline significant reduced risk of eczema (adjusted OR 0.49, 95% CI 0.24-1.01, P=0.05) and D. pteronyssinus sensitization (adjusted OR 0.42, 95% CI 0.17-1.08, P=0.07). Geohelminths and intestinal microflora were not significantly associated with any of the outcomes measured. CONCLUSION AND CLINICAL RELEVANCE: Among young children in a developing country, we found evidence to support the hypothesis of a protective effect of H. pylori infection on the risk of allergic disease. Further investigation of the mechanism of this effect is therefore of potential therapeutic and preventive value.