Neonatal thymectomy (NTx) in mice induces a group of alterations in the immune system homeostasis that results in the development of a variety of organ-specific autoimmune diseases such as gastritis, thyroiditis, oophoritis and orchitis. Given the importance of self-antigen expression in thymus for the control of autoreactive cells and generation of regulatory cells, we have compared the expression of parietal cell antigen in two strains of mice with the same H-2: BALB/c (susceptible to develop gastritis after NTx) and DBA/2 (resistant). We detected mRNA of HK-ATPase alpha and beta chains in day 1 thymi of both strains. Fifty percent of BALB/c mice presented mRNA levels similar to DBA/2. However, lower mRNA levels were found in the remaining BALB/c mice that may correspond to those that would develop AIG after NTx. Since the presence of the antigen in periphery is also necessary for the induction of regulatory cells, we have compared both strains observing in day 1 stomachs from resistant DBA/2 strain, a significantly higher content of positive cells for HK-ATPase subunits than stomachs from susceptible BALB/c strain. Also, the presence of antinuclear Abs in NTx BALB/c mice makes this model a useful experimental system for analyzing the responsible mechanisms breaking the non-specific self-tolerance.