UNLABELLED: Many environmental, genetic, and epigenetic variables are considered to influence the evolution of cow's milk allergy (CMA). The gastro-intestinal microbiota may play a direct role in or inhibit tolerance development. In this study, we planned to evaluate the presence of previously identified risk factors for microbiota composition. This study used a cross-sectional electronic survey in Turkiye, utilizing a national convenience sample of 270 children with CMA, as reported by their caregivers, and 2154 healthy controls. We developed a web-based questionnaire to gather information on pregnancy and maternal-related factors, delivery mode, feeding patterns, antibiotic use, and the presence of pets in the home. The risk factors affecting CMA were maternal age (OR 0.897
0.862-0.934, p <
0.01), presence of maternal allergic disorders (OR 3.070
1.891-4.983, p <
0.001) and in both parents (OR 3.831
1.202-12.210, p <
0.001), maternal weight at conception (OR 1.016
1.003-1.030, p <
0.05), maternal weight gain during pregnancy (OR 1.033
1.012-1.056, p <
0.01), (absence of a) pet at home (OR 1.394
1.003-1.938, p <
0.05), intrapartum antibiotic use (OR 1.469
1.092-1.975, p <
0.05), antibiotic use during the first 6 months of life (OR 1.933
1.306-2.863, p <
0.001), and number of householders (OR 0.794
0.650-0.969, p <
0.05). CONCLUSION: In addition to allergic disorders in parents, maternal weight and weight gain during pregnancy, intrapartum and first 6 months of life antibiotic use, and the presence of pets at home were found to be microbiota-related risk factors in children with CMA. Potential strategies related to microbiota composition may contribute positively to the disease's development and progression. WHAT IS KNOWN: • The gut microbiome contributes to the development of cow milk allergy, and disrupted microbiota maturation during the first year of life appears to be common in pediatric food allergies. • Factors that influence an infant's microbiota within the first 1000 days and the relationship between these factors and microbiota may enhance allergy diagnosis, prevention, and treatment. WHAT IS NEW: • Besides parental allergy disorders, maternal weight and weight gain during pregnancy, antibiotic use during intrapartum and first six months of life, and the presence of pets at home were identified as microbiota-related risk factors in children with CMA.