Pax6 genes are highly conserved and important for eye development. Vertebrates predominantly produce two alternatively spliced Pax6 isoforms, Pax6 and Pax6-5a. Pax6-5a differs from Pax6 by the presence of 14 additional amino acids encoded by exon 5a. These additional amino acids occur in the Pax6 paired domain and thus influence its DNA-binding properties. However, little is known about Pax6-5a's physiological functions. Here we establish murine embryonic stem (ES) cell lines in which expression of either the human Pax6 or Pax6-5a isoform is negatively controlled by tetracycline. We report that, in contrast to Pax6 expression, Pax6-5a expression strongly induces ES cells to differentiate into neurons. Moreover, using DNA microarray analysis, we have identified the transcription factor basic helix loop-helix domain containing, class b2 (bHLHb2) in Pax6-5a-expressing ES cells. Our Pax6 isoform-expressing ES cell lines may serve as useful models for identifying Pax6-regulated genes that are important for neurogenesis and/or eye development.