In the central nervous system, acquisition of regional specification is an important developmental process. The regional specification is reflected by restricted and overlapping expression of homeobox genes, which are regulators of this event. Here, we detail the expression pattern of Lmx1b during late embryonic brain development and show that this gene is expressed in multiple regions and diverse sets of neurons. Noteworthy, the Lmx1b expression domain is shared by Ptx2 in posterior hypothalamic regions and by Ptx3 in the dopaminergic neurons of the ventral midbrain. In addition, the mutual cofactor Ldb1 is expressed in these regions. The expression of these gene sets is maintained in the adult brain. The subthalamic nucleus, where Lmx1b is coexpressed with Ptx2, and the substantia nigra/ventral tegmental area, where Lmx1b is coexpressed with Ptx3, are both ancillary nuclei of the motor control circuitry, but use different neurotransmitters. These data point to a combinatorial gene network that allows Lmx1b to diversify its regulatory actions by cooperation with specific Ptx genes.