AbstractWe describe here the prenatal telencephalic expression of Dlx6 RNA and β‐galactosidase driven from a mutant Dlx6 locus. The mutant Dlx6 allele, which we believe is either a null or severe hypomorph, has an IRES‐lacZ‐neomycin resistance cassette inserted into the Dlx6 homeobox coding sequence (Dlx6LacZ). We compared expression from the Dlx6‐lacZ (Dlx6LacZ) allele in heterozygotes (Dlx6LacZ/+), with the expression of Dlx1, Dlx2, Dlx5 and Dlx6 RNA. Like these wild‐type alleles, Dlx6LacZ is expressed in the developing ganglionic eminences, and their derivatives. Unlike the other Dlx genes, Dlx6 and Dlx6LacZ expression is not readily observed in tangentially migrating interneurons. In addition to Dlx6's expression at later stages of differentiation of many basal ganglia nuclei, it shows particularly robust expression in the central nucleus of the amygdala. Histological analysis of Dlx6 mutants (Dlx6LacZ/LacZ) shows that this homeobox transcription factor is required for molecular properties of the striatum, nucleus accumbens, olfactory tubercle, and central nucleus of the amygdala. For instance, we observed reduced of Golf, RXRγ, and Tiam2 expression in the striatum, and reduced Dlx5 expression in the central nucleus of the amygdala. RNA expression array analysis of the E18.5 striatum was useful in identifying the transcription factors that are expressed in this tissue, but did not identify major changes in gene expression in the Dlx6LacZ/LacZ mutant. J. Comp. Neurol. 519:2320–2334, 2011. © 2011 Wiley‐Liss, Inc.