Pax6 is a transcription factor that regulates the development of the visual, olfactory, and central nervous systems, pituitary, and pancreas. Pax6 is required for induction, growth, and maintenance of the lens; however, few direct Pax6 target genes are known. This study was designed to identify batteries of differentially expressed genes in three related systems: 8-week old Pax6 heterozygous lenses, 8-week old Pax6 heterozygous eyes, and transgenic lenses overexpressing PAX6(5a), using high throughput cDNA microarrays containing about 9700 genes. Initially, we obtained almost 400 differentially expressed genes in lenses from mice heterozygous for a Pax6 deletion, suggesting that Pax6 haploinsufficiency causes global changes in the lens transcriptome. Comparisons between the three sets of analyses revealed that paralemmin, molybdopterin synthase sulfurylase, Tel6 oncogene (ETV6), a cleavage-specific factor (Cpsf1) and tangerin A were abnormally expressed in all three experimental models. Semiquantitative reverse transcription (RT)-PCR analysis confirmed that all five of these genes were differentially expressed in Pax-6 heterozygous and Pax6(5a) transgenic lenses. Western blotting and immunohistochemistry demonstrated that paralemmin is found at high levels in the adult lens and confirmed its down-regulation in the Pax6(5a)-transgenic lenses. Collectively, our data provide insights into the genetic programs regulated by Pax6 in the lens.