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Background Undesirable immunological responses to alimentary allergens are one of the hallmarks of atopic diseases. The prevalence of common food allergens is dissimilar among different communities with distinct nutritional habits and genetic characteristics. Aim To assess the prevalence of the most common food allergens in Iran, using different reliable studies. Methods All studies determining sensitization to common food allergens that were indexed in PubMed, Web of Science, Google Scholar, ProQuest, Scopus, Iran Medex, and Magiran were included in this review. To perform a meta-analysis, STATA 14 and metaprop command was applied. A logistic-normal random-effects model with Freeman–Tukey double arcsin transformation was applied to combine the findings of different studies and evaluate their heterogeneity. Random pooled estimate (ES) (pooled prevalence), 95% confidence interval (95% CI) and p-value were determined. Results A total of 23 studies with data from a total of 6126 children and adults met the inclusion criteria for entering this meta-analysis. The respective pooled prevalence of a positive family history of allergy and positive specific IgE to at least one food allergen was 72% (95% CI: 66–77%) and 41% (95% CI: 33–49%), respectively. Our results in the total population revealed that allergic sensitization to egg yolk, cow’s milk (CM), egg white, and wheat were 25% (95% CI: 16%–35%), 24% (95% CI: 19–29%), 23% (95% CI: 18%–28%), and 9% (95% CI: 6%–14%), respectively. Walnut, peanut, and soybean sensitization was detected in 23% (95% CI: 17%–31%), 23% (95% CI: 13%–33%), and 20% (95% CI: 12%–28%) of patients, respectively. Random pooled ES for sensitization to shrimp and fish was 32% (95% CI: 21–45%) and 12% (95% CI: 6–20%), respectively. The result of analysis in different age groups revealed that allergic sensitization to milk, egg white, and egg yolk declines in higher age groups; while shrimp sensitization increases in older patients. In patients with atopic dermatitis, egg white was the most frequent food allergen 29% (95% CI = 18–42%); while wheat was the least frequent 8% (95% CI = 4–14%). Conclusions Considering the prevalence of different food allergens, the results of the current meta-analysis revealed that egg yolk and cow’s milk had the second and third rate after shrimp, respectively. The high prevalence of sensitization to shrimp may be attributed to its high consumption in coastal areas and/or cross-reactivity of shrimp with some aeroallergens such as mites.