Objectives: Polyunsaturated fatty acids (PUFAs) are involved both in immune system regulation and inflammation. The aim of this prospective study was to evaluate the association between maternal dietary intake of PUFAs during pregnancy and atopic dermatitis (AD) and food allergy (FA) in their children up to 7–9 years of age. Material and Methods: The study population consists of 557 mother–child pairs from the Polish Mother and Child Cohort (REPRO_PL). Based on the Food Frequency Questionnaire completed between the 20–24th weeks of pregnancy, n-3 and n-6 PUFAs as well as n-6:n-3 fatty acid ratio were estimated using food composition tables. Children’s health examinations at the age of 1, 2, and 7–9 years were performed by an allergist. Generalized estimating equations were performed in order to assess the prevalence of AD and FA at 3 time points. Independent variables in the equation were n-3, n-6 PUFAs and n-6:n-3 PUFAs ratio. In addition multivariate models were performed to assess the association of PUFAs with AD and FA. Results: The prevalence of AD was 37%, 26% and 21% and FA 26%, 22% and 22% at age of 1, 2 and 7–9 years, respectively. Higher n-6:n-3 fatty acid ratio correlated with higher prevalence of AD at age of 7–9 years (p < 0.07). In multivariate model n-6 PUFAs were significantly associated with increased risk of persistent FA (OR = 1.5, 95% CI: 1.1–2.1). Conclusions: These results may contribute to the existing knowledge on the impact of maternal diet during pregnancy on children’s optimal health, however further studies are needed before drawing conclusions and creating clinical practice guidelines. Int J Occup Med Environ Health. 2023;36(3):428–36