Experimental aggregation chimeric mice offer a perspective on cell lineage relationships that is complementary to that of prospective tracing methods such as dye injections or recombinant retroviruses. To create a lineage map of cerebral cortex, the position and genotype of cortical neurons in three-dimensional space were reconstructed with the aid of a computer-assisted mapping system. Chi-square statistical analyses indicate that the spatial distribution of cell lineages in the cerebral cortex is highly nonrandom. When individual dimensions are analyzed separately, a high degree of order is found in the spatial distribution of neuronal genotype ratios in the anterior-posterior dimension but not in the medial-lateral dimension. This suggests an arrangement of lineage-related neurons into “slabs” or “stripes” of cells that are organized in the plane perpendicular to the neuraxis. Additionally, a highly significant variation in genotype ratios was found in the radial dimension (i.e., among cortical cell layers). These data suggest the hypothesis that separate sets of progenitor cells give rise to the superficial and deep layers of cortex. Taken together, our data are consistent with a picture of the developing nervous system in which early developmental restrictions to cell mixing set up boundaries that may be of considerable developmental genetic importance.