Background: Recognition of specific allergens triggering immune response is key for the appropriate prescription of allergen-specific immunotherapy (SIT). This study aimed at evaluating the impact of using the commercially available microarray ImmunoCAP ^TM ISAC 112 (Thermo Fisher Scientific) on the etiological diagnosis and SIT prescription compared to the conventional diagnostic methods in patients with allergic rhinitis/rhinoconjunctivitis and/or asthma. Methods: 300 patients with respiratory allergic disease, sensitized to three or more pollen aeroallergens from different species, as assessed by skin prick-test (SPT) and specific IgE assays (sIgE), were included in this multicentric, prospective observational study. SPT and a blood test were performed to all patients. Total serum IgE, sIgE (ImmunoCAP ^TM) for allergens found positive in the SPT and sIgE allergen components (ImmunoCAP ^TM ISAC 112) were measured. Results: According to SPT results, the most prevalent pollen sensitizers in our population were Olea europaea followed by grass, Platanus acerifolia and Parietaria judaica. The molecular diagnosis (MD) revealed Ole e 1 as the most prevalent pollen sensitizer, followed by Cup a 1, Phl p 1, Cyn d 1, Par j 2, Pla a 1, 2, and 3 and Phl p 5. Immunotherapy prescription changed, due to MD testing, in 51% of the cases, with an increase of prescription of SIT from 39% to 65%. Conclusion: The identification of the allergen eliciting the respiratory disease is essential for a correct immunotherapy prescription. The advances in allergen characterization using methods such as the commercial microarray ImmunoCAP ^TM ISAC 112 can help clinicians to improve SIT prescription.