Mice homozygous for lpr and gld accumulate CD4(-)CD8(-) (double-negative, DN) B220(+)CD5(lo)Thy-1(lo) alpha beta T cells in the spleen and lymph nodes (LN), while mucosal gut T cells are normal. To study other mucosa-associated T cell populations, we examined T cell subsets separated according to expression of alpha beta T cell receptor, CD4, CD5, CD8, Thy-1 and B220 in the lung and the female genital tract (FGT) of adult MRL lpr, C3H lpr and C3H girl mice. alpha beta T cell accumulation was detected in both the FGT and the lungs of lpr and gld mice but, in contrast to the spleen and LN, equal proportions of DN B220(+) and CD4(+) of CD8(+) (single-positive, SP) B220(-) T cells were observed in these sites, and the T cells had an increased expression of Thy-1 and CD5. Staining for CD44, L-selectin, and CD45RB revealed a higher percentage of effector/memory T cells in lpr and gld lungs and FGT compared to spleens and LN. CD69 expression suggested chronic activation of DN and SP T cells in lpr and girl lungs and FGT. Thus, we show that FGT and lung resident T cells are affected by lpr and gld mutations, but that their phenotypes are distinct from those of systemic T cells. These data suggest that T cells associated with FGT and lung mucosal tissues represent a separate lineage from systemic T cells, and/or that the abnormal T cells in lpr and gld mice are selected against in mucosal surfaces exposed to environmental antigen.