It is over 100 years since Brodmann proposed the homology of layer and area structure of the cerebral cortex across species. His proposal was based on the extensive comparative analyses of various mammalian brains. Although such homology is now well accepted, the recent data in our laboratory showed striking variations of gene expression patterns across areas and species. Are cortical layers and areas really homologous? If they are, to what extent and how are they similar or different? We are trying to answer these questions by identifying the homologous neuronal types common to various areas and species. Toward this goal, we started to classify the cortical pyramidal neurons by expression of particular sets of genes. By using fluorescent double in situ hybridization combined with retrograde tracers, we are characterizing the gene expression phenotypes and projection specificity of cortical excitatory neuron types. In this review, I discuss the recent findings in our laboratory in light of the past and present knowledge about cortical cell types, which provides insight to the homology (and lack thereof) of the mammalian neocortical organization.