Pediatric allergic diseases, affecting 20% of children and adolescents globally, present a growing concern. Allergic rhinitis, asthma, atopic dermatitis, and food allergy exhibit different clinical expressions and severity and are influenced by genetic and environmental factors. Traditional genetic studies faced challenges, leading to the emergence of epigenomic studies. Identifying different methylation patterns in different biological samples, from cord blood to salivary samples, provides unique epigenomic signatures, aligning with the notion of atopic march. Despite current limitations, omics sciences promise strides in pediatric allergy diagnosis and care, paving the way for early diagnosis, biomarker identification, better definition of endotypes and disease trajectories, and precision medicine. Future directions will hopefully lead to the definition of predictive methylation risk scores through multicenter longitudinal studies, exploring tissue and age-specificity of epigenomic variants.