Background To date, the effects of exclusive breastfeeding duration and timing of solid food introduction on allergy prevention are unclear. The aim of this study was to determine the effect of variable feeding practices on intestinal inflammation in infants using faecal eosinophil cationic protein as a surrogate marker and to assess whether faecal eosinophil cationic protein is associated with serum immunoglobulin E. Methods Subjects (n=206) were enrolled from the Prediction of Allergies in Taiwanese CHildren (PATCH) birth cohort study. Stool samples were collected at 6 and 12 months for determining eosinophil cationic protein, and blood was collected for determining total and allergen-specific immunoglobulin E at 12 months. We compared these biomarkers between infants with variable exclusive breastfeeding duration and infants introduced to solid foods at various periods. The association between faecal eosinophil cationic protein, total serum immunoglobulin E and specific immunoglobulin E was also analysed. Results Faecal eosinophil cationic protein was significantly higher in exclusively breastfed infants compared with formula-fed infants and infants who were not exclusively breastfed at 6 months of age (P6 months did not reduce serum immunoglobulin E, but rather increased intestinal inflammation. Faecal eosinophil cationic protein was not associated with total serum immunoglobulin E and specific immunoglobulin E and might not be a useful indictor of immunoglobulin E sensitization in infancy.