Background: In children, indoor allergens play a significant role in the development of asthma. Allergen immunotherapy for the treatment of allergic respiratory diseases has traditionally been administrated by subcutaneous Immunotherapy (SCIT) injections, with certain precautions in administration. Sublingual Immunotherapy (SLIT) could be an alternative to SCIT. Objectives: To evaluate the efficacy, safety and cost of SLIT versus SCIT among asthmatic children. Patients and methods: 46 asthmatic children were divided into two groups. Group 1 received SLIT and group 2 received SCIT with close follow up of the patients every 3 months for 9 months regarding the efficacy and safety of allergen immunotherapy using asthma symptoms score, asthma medication scores and quality of life using a validated questionnaire. A cost-effectiveness analysis was done for both routes at the end of the study. Results: Both routes have nearly equal effects on the course of bronchial asthma. SLIT was the easier route of administration (painless and not needing attendance at the doctor's clinic for each dose). Even though its direct cost was more than SCIT, it eliminates the indirect costs of travel expenses for each dose, stable for a longer time in higher temperatures, with less probability of contamination. Conclusion: Allergen immunotherapy in addition to controller medicines significantly improves both symptoms and medication scores with minimal side effects in atopic asthmatic children with the advantage of SLIT over SCIT in this age group.