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A significant increase in lymphocyte apoptosis was detected by the TUNEL method in the thymus, spleen, and Peyer's patches (PP) following intraperitoneal (i.p.) administration of dimethyl sulfoxide (DMSO) (treatment, n = 47; control, n = 8). Interestingly, administration of low doses of DMSO caused apoptosis in only the PP, and suggested that i.p. administration of DMSO induced apoptosis for each lymphoid organ in a dose dependent manner. Moreover, in the early stage during the apoptotic change, a characteristic localization of lymphocytes undergoing apoptosis was observed. Briefly, early apoptosis occurred predominantly in the cortical mid-zone of the thymus, white pulp of the spleen, and germinal centers of PP. With increased time following administration, however, lymphocytes throughout lymphoid tissues, independent of characteristic localization during the early stage, seemed to undergo apoptosis, resulting in the severe loss of lymphocytes. In fact, the relative spleen weight significantly decreased at 24 h following DMSO administration (n = 7; P < 0.001 versus 8 control mice). Taken together, these results showed for the first time that the in vivo administration of DMSO to mice caused apoptosis in lymphoid organs, and also demonstrated that the apoptotic behavior varied between different lymphoid organs.