Background: The advent of allergen biochips has resulted in the description of complex sensitization profiles in allergic children. The low volume required for a biochip scan facilitates the analysis of local samples. The objective of this work was to develop an experimental protocol to detect specific IgE (sIgE) in fecal samples using allergen biochips and to evaluate its predictive value for the subsequent development of allergic diseases. Method: The analysis was carried out on 21 stool samples collected between birth and 14 weeks of age from infants included in the Primibiota protocol (NCT02738411). The occurrence of food allergies, asthma, or atopic dermatitis at 1 year of age was recorded as part of the cohort follow-up. We developed and optimized a stool extraction protocol, followed by freeze-drying and solubilization. sIgE responses were investigated with a 300-allergen biochip containing whole extracts and molecular allergens, and confirmed by capillary Western blot with nano-immunoassay. The local eosinophilic component was explored by measuring the concentration of Eosinophil-Derived Neurotoxin (EDN) with a fluoroenzymoimmunoassay. Results: sIgE was detected in all tested samples. With respect to prevalence, the main sIgE responses were detected with animal food (21/21), plant food (20/21), pollens (19/21) and animal dander (15/21) extracts and molecular allergens. The presence of sIgE was confirmed by Western blot for cow's milk proteins. Quantitatively, fecal EDN and sIgE concentrations were significantly different in infants who would later develop atopic disease. Conclusion: Exploration of the sIgE and eosinophilic response can be performed non-invasively in the stool of the infant. Our results suggest a predictive value of this investigation for the subsequent development of asthma, food allergy or atopic dermatitis.