Nuclear factor kappa B (NF-κB) is a key transcription factor controlling inflammation, innate immunity, and tissue integrity. NF-κB is activated by IκB kinase (IKK) in response to pro-inflammatory stimuli but is also found to be chronically activated in many inflammatory diseases accompanied by tissue destruction. To study the effects of chronic NF-κB activation in intestinal epithelium, we generated IKKβ(EE)(IEC) transgenic mice which express constitutively active form of IKKβ in their intestinal epithelial cells (IEC). In this chapter, we describe three different methods that we applied for analysis of NF-κB activation in IEC of IKKβ(EE)(IEC) transgenic mice: immunohistochemistry (IHC), nuclear fractionation, and chromatin immunoprecipitation (ChIP). These methods can be also applied to analyze NF-κB activation in mouse intestinal tissue in general.