The Nkx-6.1 homeodomain transcription factor was previously shown to be expressed in ventral neural progenitor cells and subsequently subsets of unidentified motor neurons during early neural development. In this study, we identify a specific subpopulation of motor neurons, the median half of the lateral motor neuron column (LMCm), that retain a strong expression of Nkx-6.1. In addition, we report novel patterns of Nkx-6.1 expression in several mesenchymal tissues surrounding Sonic hedgehog (Shh)-expressing cells, including ventral spinal meninges, esophageal mesenchyme, and dorsal tracheal mesenchyme. Whereas Shh signaling is required for Nkx-6.1 expression in the ventral neural tube and spinal meninges, an Shh-independent pathway appears to operate in regulating Nkx-6.1 expression in the foregut. The persistent and robust expression of Nkx-6.1 in motor neurons and mesenchymal cells suggests an important role for Nkx-6.1 in controlling cell fate specification and differentiation. genesis 27:6-11, 2000.