Mice lacking a functional Jak2 allele die embryonically, indicating the mandatory role of Jak2 in basic developmental cellular transcription. Currently however, the downstream target genes of Jak2 are largely unknown. Here, in vitro conditions were created using a cell line lacking Jak2 expression. Microarray analysis was then used to identify genes that are differentially expressed as a result of the presence, or absence, of Jak2. The data identified 621 Jak2-dependent genes as having at least a 2-fold change in expression. Surprisingly, these genes did not require ligand-dependent activation of Jak2, but merely its expression in the cell. Thirty-one of these genes were found to have a greater than 7-fold change in expression levels and a subset of these were further characterized. These genes represent a diverse cluster of ontological functions including transcription factors, signaling molecules and cell surface receptors. The expression levels of these genes were validated by Northern blot and/or quantitative RT-PCR analysis in both the Jak2 null cells and cells expressing a Jak2 dominant negative allele. As such, this work demonstrates for the first time that, in addition to being a key mediator of ligand-activated gene transcription, Jak2 can perhaps also be viewed as a critical mediator of basal level gene expression.