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Background Food allergy has emerged as a significant medical problem in the last decades. Probiotics' effects on food allergies have brought contradictory results. The present study aimed to assess the probiotic's results in cytokines related to food allergy through meta-analysis. Methods Science Direct and Scopus search engines were searched for relevant studies published from 2008 to 2019 without language exclusion. Some experiments were selected from articles evaluating the effect of probiotics on food allergy through pre-clinical studies, with the results published in peer-reviewed journals, with any dispersion measure. Cytokines values were selected as outcomes. We used metaregression to study the probiotic effect in each cytokine and the influence of some experimental design factors. Results We obtained a total of 13 studies that met the criteria for the meta-analysis. Probiotics download the regulation of IL-4 and IgE and the upload regulation in IL-6 and TGF-β compared to controls. Lactobacillus is a species that helps in the restoration of IL-4 levels. Animal age, probiotic concentration, and microorganism specie affect the probiotic effect in INF-γ. Conclusion The meta-analysis evidenced, in pre-clinical studies, the effects of probiotics on cytokines related to food allergy.