Introduction: Food protein-induced allergic proctocolitis (FPIAP) is the most common non-IgE-mediated food allergy and it varies between 4% and 8% in infants. The aim of the study was to evaluate the potential association between FPIAP in infants and maternal daily consumption of homemade fermented foods (FFs) during pregnancy. Methods: Two hundred and seven infants were included in this case-control study, 106 with physician-diagnosed FPIAP (FPIAP group) and 101 age- and gender-matched healthy infants (control group), together with their mothers. The frequency and diversity of the 8 most consumed homemade FFs in traditional Turkish cuisine and daily maternal consumption of these during pregnancy were evaluated retrospectively using a structured questionnaire. Results: Rates of vaginal delivery, maternal smoking during pregnancy, educational status, and monthly household income were higher in the FPIAP group than the control group (p = 0.046, p = 0.014, p < 0.001, and p = 0.009, respectively). The 3 most common daily-consumed FFs during pregnancy were, in order, yogurt, cheese, and tarhana. The diversity of daily-consumed FFs during pregnancy (p = 0.004) and the consumption of the 3 most common FFs (p = 0.011) were lower in the FPIAP group than in the control group. Maternal smoking during pregnancy (odds ratio [OR]: 2.97, 95% confidence interval [CI]: 1.19–7.41, p = 0.019) and a higher maternal educational status (OR: 3.34, 95% CI: 1.63–6.84, p = 0.001) increased the risk of FPIAP at multivariate logistic regression, while the diversity of maternal FF consumption was protective against FPIAP (OR: 0.75, 95% CI: 0.58–0.96, p = 0.025). Conclusion: Daily maternal consumption of yogurt, cheese, and tarhana during pregnancy was less common in FPIAP. The diversity of traditional Turkish homemade FFs may reduce the risk of FPIAP, whereas maternal smoking and a higher maternal educational status were associated with an increased risk of FPIAP.

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