Despite its small size, the arcuate nucleus of the hypothalamus has a critical role in regulating energy homeostasis. We have begun to define genetic approaches to express genes in specific cell types within the developing arcuate nucleus, to allow precise molecular perturbations of these cells. Furthermore, our analysis aims to contribute to defining the transcriptional networks that regulate the development of function of the arcuate neurons. Here, we define the neuronal cells types within the arcuate that express Nkx2.1 and Dlx homeobox genes. In addition, we used mice expressing Cre recombinase from the Dlx5/6 intergenic enhancer (Dlx5/6i) and from the Nkx2.1 locus to follow the fate of embryonic cells expressing these genes within the arcuate nucleus. We demonstrate that NKX2.1+ cells and their lineages are broadly expressed in arcuate neurons [γ-aminobutyric acid (GABA)+, neuropeptide Y (NPY)+, proopiomelanocortin (POMC)+, tyrosine hydroxylase (TH)+] and glia (tanycytes). On the other hand, DLX+ cells and their lineages mark only GABA+ and TH+ (dopaminergic) neurons, and Dlx1–/– mutants have fewer TH+ neurons. These results have implications for the genetic control of arcuate development and function and for the utility of the Nkx2.1-Cre and Dlx5/6i-Cre mouse lines to alter gene expression in the developing arcuate. J. Comp. Neurol. 517:37–50, 2009. © 2009 Wiley-Liss, Inc.