Spontaneous colitis resembling ulcerative colitis developed in 3 of 10 independent TCR transgenic (Tg) mouse lines maintained under specific pathogen-free conditions. All three susceptible lines were CD4 lymphopenic, whereas resistant lines had normal numbers of CD4+ T cells. Thus, cytochrome c-specific 5C. C7 TCR Tg mice developed colitis only when crossed onto a SCID-or Rag-1-deficient background. A second line of lymphopenic cytochrome c-specific Tg mice bearing the AND TCR also developed colitis. In both cases, CD4+ T cells expressing the Tg-encoded TCR were preferentially activated in inflamed colons compared with lymph nodes or spleens. In contrast, Tg+ CD4+ T cells remained quiescent in both inflamed and unaffected colons in another line of susceptible Tg mice carrying a TCR specific for myelin basic protein, suggesting a fortuitous cross-reactivity of the IE k-restricted cytochrome c-reactive AND and 5C. C7 TCRs with an Ag present in the gut. The percentage of CD4+ T cells expressing only endogenous TCR α-chains was increased consistently in inflamed colons in AND as well as 5C. C7 Rag-1−/− TCR Tg mice, suggesting that polyclonal CD4+ T cells were also involved in the pathogenesis of spontaneous colitis. Moreover, our data indicate that some α-chain rearrangement was still occurring in TCR Tg mice on a Rag-1−/− background, since activated CD4+ T cells expressing endogenously rearranged α-chains paired with the Tg-encoded β-chain were detected consistently in the colons of such mice.