The role of basophils in allergic rhinitis (AR) has been studied extensively; however, there are very few reports on changes in basophils after allergen-specific immunotherapy (SIT). To examine the changes and correlation of peripheral blood basophils and the therapeutic effect in patients with AR during allergen-SIT. A total of 77 patients with AR who were allergic only to house dust mites received allergen-SIT. At 3 time points, patients underwent testing for the percentage and activation rate of basophils in peripheral blood, skin index (SI) measurement, visual analog scale (VAS) assessment, and rhinoconjunctivitis quality of life questionnaire (RQLQ) evaluation. The results were compared to a control group with congenital preauricular fistula. (1) Before treatment, the percentage and activation rate of basophils in patients with AR were significantly higher than those in controls. There was no significant difference in the percentages and activation rates of basophils at the 3 time points. (2) The SIs, VAS, and RQLQ scores of the patients immediately after treatment and 2 years posttreatment decreased significantly compared to those before treatment; the SI, VAS, and RQLQ scores of the patients 2 years posttreatment increased significantly compared with those immediately after treatment. (3) There was no correlation between the patients' basophil activation rate and percentage and the SI, VAS, and RQLQ scores at all time points. The percentage and activation rate of basophils were higher in patients with AR than in controls. The values did not change significantly after allergen-SIT and showed no correlation with treatment effectiveness. Therefore, the frequency and activation rate of basophils cannot be used as criteria for assessing the effectiveness of allergen-SIT for house dust mites. Allergen-SIT is effective for the management of AR, but the effect declines after the completion of therapy.