N uclear factor-KB (NF-κΒ) is a cytoplasmic transcription factor that plays a key role in inducible gene expression during activation of the innate immune response. Cell stimulation with bacterial endotoxins, viral replication, or by cytokine cascades activates signaling pathways to converge on NF-κΒ. Activated NF-κΒ, in turn, initiates a ge nomic response controlling expression of cytokines, transcription factors and anti-apoptotic proteins whose action affect immune responses, control signaling pathways or influence cell survival. Although the mechanisms for activation and termination of this signaling pathway have been intensively investigated, we are now only beginning to identify the spectrum of genes under its control. Various approaches have been used to identify NF-κΒ dependent genes, including candidate gene study, mRNA expression profiling, and “ChIP on ChIP”. Here we describe our experience with mRNA profiling of engineered epithelial cells that inducibly ex press a NF-κΒ dominant negative inhibitor. The insights gained from these studies are dis cussed, including the identity of genetic targets under its control, the biological pathways af fected, and our unanticipated findings for temporal coordination of waves of NF-KB-dependent gene expression.