SDF-1/CXCR4 plays an important role in promoting survival, expansion, and differentiation of T cell progenitors. The present study investigates the mechanism by which estrogen inhibits SDF-1alpha expression in mouse thymus. Mouse estrogen enhanced transcript (mEET) is endogenously expressed in a mouse thymus epithelial cell line 1 (MTEC1). In MTEC1 cells that express the transfected sense mEET, the SDF-1alpha transcription and its chemotactic activity were profoundly inhibited. Conversely, in MTEC1 that express the transfected anti-sense mEET, the SDF-1alpha transcription and its chemotactic activity were substantially augmented. Moreover, we disclosed that mEET inhibited the production of SDF-1alpha by its suppression of NF-kappaB translocation into nucleus. Using a combinatorial induction of doxycycline (Dox) and 17beta-estradiol (E2) on the sense and anti-sense mEET transfectants, it was demonstrated that an increase of mEET expression enhanced E2-induced inhibition of SDF-1alpha production, while a blockade of mEET expression alleviated E2-induced inhibition of SDF-1alpha production. In conclusion, the E2-imposed suppression of SDF-1alpha production is partly mediated by mEET involved signaling pathway.