Clinical experiences in vitro and clinical studies have demonstrated the curative potency and safety of Citrus/Cydonia compositum in seasonal allergic rhinitis treatment. Objectives: To compare the efficacy and safety of two routes of administration (nasal spray versus subcutaneous injections). Methodology: Design. A national, randomized and comparative clinical trial with two parallel groups. Participants: 23 patients fulfilled the study requirements. Intervention: After a one- or two-week wash-out period, 23 patients were randomized, to a 6-week treatment period. Outcomes: Immunological and symptom severity changes and safety. Immunologic outcome assessments were blinded to group assignment. 23 patients were randomized and from 22/23 patients (11 in each group) blood samples were analyzed before and after treatment. Conclusion: Both routes of administration demonstrate immunological and clinical effects, with larger inflammatory and innate immunological effects of the nasal spray route and larger allergen-specific clinical effects of the subcutaneous route, and are safe.