Combining gene expression data with morphological information has revolutionized developmental neuroanatomy in the last decade. Visualization and interpretation of complex images have been crucial to these advances in our understanding of mechanisms underlying early brain development, as most developmental processes are spatially oriented, in topologically invariant patterns that become overtly distorted during brain morphogenesis. It has also become clear that more powerful methodologies are needed to accommodate the increasing volume of data available and the increasingly sophisticated analyses that are required, for example analyzing anatomy and multiple gene expression patterns at individual developmental stages, or identifying and analyzing homologous structures through time and/or between species. Three-dimensional models have long been recognized as a valuable way of providing a visual interpretation and overview of complex morphological data. We have used a recently developed method, optical projection tomography, to generate digital three-dimensional models of early human brain development. These models can be used both as frameworks, onto which normal or experimental gene expression data can be mapped, and as objects, within which topological morphological relationships can be investigated in silico. Gene expression patterns and selected morphological structures or boundaries can then be visualized individually or in different combinations in order to study their respective morphogenetic significance. Here, we review briefly the optical projection tomography method, placing it in the context of other methods used to generate developmental three dimensional models, and show the definition of some CNS anatomical domains within a Carnegie stage 19 human model. We also map the telencephalic EMX1 and PAX6 gene expression patterns to this model, corroborating for the first time the existence of a ventral pallium primordium in the telencephalon of human embryos, a distinct claustroamygdaloid histogenetic area comparable to the recently defined mouse primordium given that name [Puelles L, Kuwana E, Puelles E, Bulfone A, Shimamura K, Keleher J, Smiga S, Rubenstein JLR (2000) Pallial and subpallial derivatives in the embryonic chick and mouse telencephalon, traced by the expression of the genes Dlx-2, Emx-1, Nkx-2.1, Pax-6, and Tbr-1. J Comp Neurol 424:409-438; Puelles L, Martínez S, Martínez-de-la-Torre M, Rubenstein JLR (2004) Gene maps and related histogenetic domains in the forebrain and midbrain. In: The rat nervous system, 3rd ed (Paxinos G, ed), pp 3-25. San Diego: Academic Press].