Aim: To study the apoptosis of Foxp3+ Treg cells following Alstonia scholaris pollen sensitization–challenge and following allergen immunotherapy. Materials & methods: Wistar rats were sensitized–challenged with Alstonia scholaris pollen and were further given intranasal immunotherapy. For the analysis of the apoptotic proteins on Treg cells by flow cytometry, multiple gating procedures were followed. Results: Allergen sensitization–challenge increases Annexin-V, Fas, FasL, caspases-8, 9, 3 cytochrome-C, APAF-1, Bax, perforin-1 and granzyme-B on Treg cells which is decreased following intranasal immunotherapy. On the other hand, Bcl-2 expression is decreased in allergy and increased by immunotherapy. Conclusion: Apoptosis of Treg cells is increased following allergen sensitization–challenge via extrinsic, intrinsic and perforin/granzyme pathways and allergen immunotherapy decreased the sensitivity to apoptosis of Treg cells.