Background <p>Emerging evidence suggests that specific allergen molecules may influence the clinical phenotype of anaphylaxis in children, but robust data are scarce. This study aimed to rigorously test the molecule-phenotype association in a large pediatric cohort and to determine the relative influence of the sensitizing molecule versus patient age on symptom presentation.</p> Methods <p>A retrospective analysis was conducted on 184 pediatric patients (0–18&#xa0;years) hospitalized for anaphylaxis. Molecular allergen-specific immunoglobulin E (IgE) profiles were determined using the ALEX² test. Symptom frequencies across different organ systems were analyzed in relation to allergen molecules and age groups using Cochran’s Q and Pearson’s χ2 tests.</p> Results <p>The most frequent molecular triggers were Ara h 2 (18.79%), Gal d 1 (9.09%), and Ana o 3 (9.09%). While significant differences in symptom distribution were observed within individual allergen molecules (<i>p</i> &lt; 0.05), no molecule-specific symptom pattern was identified. In contrast, age significantly influenced respiratory symptom prevalence, with a higher frequency in older children compared to infants (<i>p</i> = 0.003). A similar trend was observed for gastrointestinal symptoms (<i>p</i> = 0.051).</p> Conclusions <p>In pediatric anaphylaxis, patient age is a more significant determinant of clinical presentation, particularly for respiratory symptoms, than the specific sensitizing allergen molecule. This suggests that clinical risk stratification and management strategies in children should prioritize age-related factors over specific molecular sensitization profiles.</p>