Signaling via the endogenous arylhydrocarbon receptor (AHR) affects proliferation, differentiation, function and gene expression of thymocytes. In the present study, we show that treatment of mouse fetal thymus lobes in organ culture (FTOC) with AHR ligands results in (a) a drastic decrease in the emigration of thymocytes in terms of numbers and types of cells, and (b) preferential emigration of CD4 −CD8 − (DN) cells expressing CD44v7- and CD44v10-containing isoforms on the cell surface. Moreover, a higher level of transcripts of various other CD44 variant isoforms (CD44v) could be detected by RT-PCR in emigrants from fetal thymi exposed to either AHR-agonist during culture. Expression of CD44v9–10-containing isoforms could be exclusively detected in DN thymic emigrants. Thus, signaling via AHR by ligands alters CD44v expression patterns in a thymocyte subpopulation. Furthermore, emigration could be decreased by the addition of anti-panCD44 antibodies to TCDD-treated FTOCs, suggesting a role for CD44 in emigration.