The mammalian cerebral cortex, although a structure of great complexity, is characterized by a high degree of organization where the proportions, spatial relationships, and properties of the various cell types are rigidly controlled. The mechanisms responsible for the creation of such a rigid distribution of cell types are not known. Lineage studies in adult rats have suggested that each of the cortical progenitor cells lining the telencephalic ventricles during embryonic development gives rise to progeny of the same phenotype (homogeneous clones). However, the possibility that homogeneous clones are the result of complex processes affecting both the final number and the phenotype of clonally related cells during development has not been investigated. In the present study, we followed the development of cortical cell lineages labeled with retroviral injections at embryonic day (E) 16 in rats of 7, 14, or 21 d of age using electron microscopy and immunocytochemistry for the neurotransmitters glutamate and GABA. We found that a significant number of cortical clones at postnatal day (P) 7 and P14, and fewer at P21, showed mixed pyramidal/nonpyramidal cell composition. We sometimes observed that "mixed" neuronal clones contained cells immunoreactive for both glutamate and GABA. In the general population of cortical cells, "bireactive" neurons represented 3.7% of all neurons at P7, 18% at P14, and 0.6% in adult rats. Although the change in the composition of neuronal clones between the third week of postnatal life and adulthood may be due to changes in the phenotype of some developing neurons, we would like to suggest that it is probably due to selective neuronal cell death.