The ALY (aly/aly) mouse, a mutant of the C57BL/6j strain, has a severe immunodeficiency because of immature development of the immune organs. Both lymph nodes and Peyer's patches are lacking and both the thymus and spleen are small. Previous microscopical observation of their thymus glands revealed the presence of an indistinct border between the cortex and medulla, the absence of Hassal's corpuscles and the reduction of the medullary epithelial cell population. However, other microscopical findings for these glands have not yet been reported. In the present study, we performed light and electron microscopical observation of the thymus and found the consistent presence of extremely irregular shaped cystic cavities lined by microvilli-bearing epithelium in the medulla. The cysts comprised ceca and did not open into adjacent capillaries, although they contained some lymphocytes and macrophages in their lumens. In the thymus glands of normal C57BL/6j mice, only some small cysts oval in shape could be inconspicuously found in the medulla. Therefore, the thymic cysts may normally regress during thymic development, however, in ALY mice, the cysts may remain because of the organ immaturity.