The human cortex is comprised of diverse cell types that emerge from an initially uniform neuroepithelium that, following neural tube closure, gives rise to radial glia, the neural stem cells of the cortex. Radial glia initially reside in the ventricular zone of the cortex, and contribute to cortical expansion which is particularly pronounced in the human compared to other mammals and non-human primates. To characterize the molecular signatures of cellular subtypes that may exist at the earliest stages of neurogenesis we performed single-cell RNA-sequencing across regions of the developing human brain. We observe similar progenitor programs across brain regions that each express region-specific transcription factors. In the telencephalon, we identify nine progenitor populations, suggesting more heterogeneity among neuroepithelial cells and radial glia than previously described, including a highly prevalent mesenchymal-like population that disappears after the onset of neurogenesis. Using velocity analysis, we find that genes implicated in various neurodevelopmental diseases drive the specification and maintenance of neuroepithelial cells and radial glia. Comparison of these progenitor populations to corresponding stages of mouse development identifies two progenitor clusters that are unique to the early stages of human cortical development. Organoid systems display a low fidelity to neuroepithelial and early radial glia cell types, but this improves as neurogenesis progresses. Overall, we provide a comprehensive molecular and spatial atlas of early stages of human brain and cortical development.The human brain consists of billions of cells across several functionally interconnected structures that emerge from the neuroectoderm. Many of these structures are substantially expanded or distinct compared to other mammals 1 , particularly the cerebral cortex, the outermost layer of the human brain responsible for perception and cognition. These differences emerge at developmental stages prior to birth 2 , and thus exploring the cell types in the developing human brain is essential to better characterize how cell types across the brain are generated, how they may be impacted during the emergence of neurodevelopmental disorders, and how human neural stem cells can be directed to specific cell types for modeling or treatment purposes. The brain exponentially increases in size after the neural tube closes 3,4 . Later in development, across brain regions, a series of similar neurogenic and gliogenic processes gives rise to the constituent cell types 5 . However, at the molecular level, the sequence of events that leads to the emergence of these progenitor cells early in development is much less well understood. In order to identify cell types and trajectories that lay the foundation for the development of the human brain, we performed single-cell RNA sequencing (scRNA-seq) using the droplet-based 10X Genomics Chromium platform on ten individuals during the first trimester of human development, spanning Carnegie Stages (CS) ...