Expression of Thy-1 and CD3 antigens on thymocytes and the nylon wool-non-adherent (nylon-nonad) fractions of peripheral lymphocytes in F344 rats was studied by flow cytometry using anti-Thy-1 and anti-CD3 antibodies. In terms of the expression and density of Thy-1 and CD3, the thymus and peripheral lymphoid tissues in rats contained different populations. Nearly all thymocytes showed a high density of Thy-1 (Thy-1(hi)); , small population with a low density of Thy-1 (Thy-1(lo)) was found in CD3 bright-positive (CD3(hi)) thymocytes. Three-color analysis with CD4, CD8 and Thy-1 revealed Thy-1(lo) thymocytes to have mainly CD4 or CD8; Thy-1(hi) thy mocytes also contained CD4 or CD8 single-positive (SP) cells as a minor population. Thus, SP thymocytes bearing CD3 were divided into two populations by evaluation of the density of Thy-1. Of peripheral CD3(+) T cells, 15% showed a low density of Thy-1(+) and the others were Thy-1(-). Both T cells responded to anti-CD3 monoclonal antibody (mAb). However, no Thy-1(hi) T cells were found in peripheral lymphoid tissues. These results suggested that SP thymocytes in rats develop with the reduction of Thy-1, but not with its loss, and are newly supplied to peripheral lymphoid tissues as the phenotype, Thy-1(lo), and are altered to Thy-1(-) T cells. Analysis of each cell size and disappearance of peripheral Thy-1(lo) T cells with age supported the above conclusion. In contrast, no Thy-1(lo) T cells were found in intestinal intra-epithelial lymphocytes (IEL), suggesting that rat IEL as well as those in mice are composed of different populations from those in peripheral lymphoid tissues.