Asymmetric divisions that produce two distinct cells play fundamental roles in generating different cell types during development. In the Drosophila central nervous system, neural stem cells called neuroblasts divide unequally into another neuroblast and a ganglion mother cell which is subsequently cleaved into neurons. Correct gene expression of ganglion mother cells requires the transcription factor Prospero. Here we demonstrate the asymmetric segregation of Prospero on neuroblast division. Prospero synthesized in neuroblasts is retained in the cytoplasm and at mitosis is exclusively partitioned to ganglion mother cells, in which it is translocated to the nucleus. Differential segregation of Prospero was also found in the endoderm. We have identified a region in Prospero that is responsible for this event. The region shares a common motif with Numb, which also shows unequal segregation. We propose that asymmetric segregation of transcription factors is an intrinsic mechanism for establishing asymmetry in gene expression between sibling cells.