C-Lmx1 has been shown to be a key regulatory gene for specification of dorsoventral pattern during vertebrate limb development. Here, we describe its earlier pattern of expression during and shortly after neurulation. Transcripts are first expressed in the mesoderm of the head process and rostral tip of the primitive streak at the late gastrula/early neurula stage (stage 4). As neurulation occurs with shaping of the neural plate, C-Lmx1 is expressed in a butterfly-like pattern in the lateral neuroectoderm. During bending of the neural plate, C-Lmx1 expression becomes localized to three areas of the bending neuroectoderm: the median hingepoint (future floor plate of the neural tube) and the paired dorsolateral regions of the neuroepithelium, including the dorsolateral hingepoints and the adjacent neuroectodermal and epidermal ectodermal components of the neural folds. After closure of the neural groove and formation of the primary brain vesicles, C-Lmx1 is expressed in the dorsal neural tube along the entire length of the neuraxis, as well as in the floor plate at the brain but not spinal cord levels. At the midbrain and rostral hindbrain levels, C-Lmx1 is heavily expressed. Here, in addition to expression in the dorsal neural tube and floor plate, it is expressed in the lateral walls of the neural tube, with the exception of the levels of rhombomeres 2 and 4. C-Lmx1 is also expressed in several other discrete domains during and shortly after neurulation, including the prechordal plate and rostral head mesenchyme, foregut endoderm, otic placode and vesicle, dorsal somitic mesoderm, midline endoderm at the level of the caudal spinal cord, mesonephroi and limb bud mesoderm.