Thymectomy on day 3 after birth (D3Tx) is understood to eliminate CD4+CD25+ regulatory T cells (Treg) from the peripheral T cell repertoire in rodents, leading to the activation of autoreactive T cells. Herein, D3Tx was performed in IQI/Jic mice, a model for Sjögren's syndrome characterized by autoimmune infiltrations into the lacrimal and salivary glands. At the age of 16 weeks, very severe lesions were observed in lacrimal tissues from thymectomized mice, suggesting that Treg preserve their immunoregulatory function in young IQI/Jic mice. In contrast, salivary lesions were comparable in the D3Tx and control groups, raising the possibility that either salivary-specific Treg escaped elimination in thymectomized mice or spontaneous lesions in IQI/Jic mice developed independently of the tolerance through Treg.