Over one-third of patients with chronic lung disease undergoing lung transplantation have pre-existing antibodies against lung-restricted self-antigens, collagen type V (ColV) and k-alpha1 tubulin (KAT). These antibodies can also develop de novo following lung transplantation and mediate allograft rejection. However, the mechanisms leading to lung-restricted autoimmunity remain unknown. Since these self-antigens are normally sequestered, tissue injury is required to expose them to the immune system. We previously showed that respiratory viruses can induce apoptosis in CD4+CD25+Foxp3+ T cells (Tregs), the key mediators of self-tolerance. Therefore, we hypothesized that lung-tissue injury can lead to lung-restricted immunity if it occurs in a setting when Tregs are impaired. We found that human lung recipients who suffer respiratory viral infections experienced a decrease in peripheral Tregs. Pre-existing lung allograft injury from donor-directed antibodies or gastroesophageal reflux led to new ColV and KAT antibodies following respiratory viral infection. Similarly, murine parainfluenza (Sendai) respiratory viral infection caused a decrease in Tregs. Intratracheal instillation of anti-MHC class-I antibodies, but not isotype control, followed by murine Sendai virus (SdV) infection led to development of antibodies against ColV and KAT, but not collagen II (ColII), a cartilaginous protein. This was associated with expansion of IFN-γ producing CD4+ T cells specific to ColV and KAT, but not ColII. Intratracheal anti-MHC class-I antibodies or hydrochloric acid in Foxp3-DTR mice induced ColV and KAT, but not ColII, immunity, only if Tregs were depleted using diphtheria toxin. We conclude that tissue injury combined with loss of Tregs can lead to lung-tissue restricted immunity.