Introduction: The prevalence of allergic asthma are increasing, and the clinical outcome and risk factors of immunotherapy in the treatment of allergy have not been well established. Especially, the impact of viral infection on cytokines in allergic inflammation has yet to be established. This study aimed to determine serum IL-3, IL-11 and IgE levels and blood eosinophil and neutrophil counts during a one-year follow up in patients with allergic asthma on immunotherapy and those on anti-asthmatic drugs only, in the presence of influenza-like illness. Materials and Methods: Sixty patients with allergic asthma were included in the prospective and comparative clinical study with randomization into two treatment groups. Each patient in the immunotherapy group was treated with subcutaneous specific immunotherapy. After patient recruitment, the serum IL-3, IL-11 and IgE levels and blood eosinophil and neutrophil counts and the frequency of influenza-like symptoms were recorded during a one-year follow up. Results: A large percentage of patients in the control group had flu symptoms compared to those in the immunotherapy group. The median serum IL-3 and the IL-11 levels were significantly higher in the immunotherapy group of patients compared to the control group. The median serum IgE level was significantly higher in the immunotherapy group of patients compared to the control group during second quarter of follow-up. Conclusion: The presence of influenza-like symptoms during allergen specific immunotherapy did not significantly change IL-3, IL-11 levels, neutrophil and eosinophil counts.