The invention discloses a knockout mouse that is homozygous for a RUNX3 null allele, as a novel model for chronic inflammatory disease. The present invention provides methods for treating T cell-related inflammatory conditions by cell therapy, gene therapy or antisense for up regulating or down regulating RUNX3. The invention further relates to methods of diagnosing and assessing predisposition to chronic inflammatory diseases. The present invention further provides methods for testing agents for effectiveness in treating and/or preventing diseases associated with chronic inflammatory or autoimmune conditions.