The cerebral cortex is one of the brain structures with the highest cell type diversity. Yet the mechanisms underlying this diversity remain elusive. While various parameters such as gene expression and chromatin accessibility can be assessed within these cells, a dimension of variability that has been largely overlooked is isoform diversity. Pax6 is a fundamental transcription factor during development of the nervous system, especially eye and cortical development. It is also a largely studied homeobox gene, but there is limited knowledge about its isoforms and their specific roles. We studied the expression pattern of different Pax6 isoforms at single-cell resolution by generating knock-in mouse lines in which Pax6 isoforms were labeled with different protein tags. Our findings reveal that the expression pattern of these isoforms is not uniform across cortical progenitor cells in the mouse brain. As development progresses, their expression patterns diverge further. This opens up the possibility that, in addition to differential gene expression, cell-specific splicing patterns may unveil a new layer of cortical progenitor heterogeneity.