Thymus organogenesis requires coordinated interactions of multiple cell types, including neural crest (NC) cells, to orchestrate the formation, separation, and subsequent migration of the developing thymus from the third pharyngeal pouch to the thoracic cavity. The molecular mechanisms driving these processes are unclear; however, NC-derived mesenchyme has been shown to play an important role. Here, we show that, in the absence of ephrin-B2 expression on thymic NC-derived mesenchyme, the thymus remains in the cervical area instead of migrating into the thoracic cavity. Analysis of individual NC-derived thymic mesenchymal cells shows that, in the absence of ephrin-B2, their motility is impaired as a result of defective EphB receptor signaling. This implies a NC-derived cellspecific role of EphB-ephrin-B2 interactions in the collective migration of the thymic rudiment during organogenesis.T hymus development in the mouse begins at E9.5 with the formation of the third pharyngeal pouches and concomitant expression of transcription factors including Hoxa3, Pax1/9, Eya1, and Six1/4 within the third pharyngeal pouch endoderm (1-4). Soon after, neural crest (NC)-derived mesenchymal cells (NCCs) from the posterior hindbrain undergo epithelial-to-mesenchymal transition (EMT), delaminate, and migrate to and surround the pouch, which simultaneously begins to grow into a separate structure containing the thymus and parathyroid primordia. By E12.5, the thymic primordium is completely detached from both the pharyngeal pouch and parathyroid. Subsequently, the bilateral lobes descend into the thoracic cavity, where they finally settle in the upper mediastinum above the heart. NCCs, which contribute to various tissues in the mouse, are also key players in thymus organogenesis. NC-derived cells have been shown to regulate patterning of the third-pouch endoderm into thymus and parathyroid-specific domains (5) and stimulate thymic epithelial cell (TEC) proliferation and maturation through production of FGFs (6). NC-derived cells also stabilize blood-vessel structures by differentiating into perivascular cells (7,8).The mechanisms that control the various morphogenetic events during early thymus organogenesis are still largely unknown, although some genes have been identified that affect these events. Hox3 and Pax1/9 transcription factors act in a pathway that is required for proper separation and/or migration of the developing thymic and parathyroid primordia from the pharynx, although the cell-type specificity of these functions is poorly understood (2, 9, 10). Splotch embryos, which have a null allele of Pax3 and are largely deficient of NCCs, also exhibit pharyngeal-pouch defects, including an ectopic thymus (5, 11). This NCC deficiency resulted in delayed separation of the thymus and parathyroid from the pharynx, and the boundary between thymus and parathyroid-fated domains was abnormal. These results strongly implicated NCC migration to the third pharyngeal pouch in patterning and morphogenesis of the thymus and parathyroids (5...