Inflammatory bowel disease (IBD) is subdivided into ulcerative colitis and Crohn's disease, which are chronic disorders. Millions of persons throughout the Western world are affected by IBD, and the condition is associated with severe morbidity and reduced quality of life for afflicted persons. The etiology is complex and not fully understood. The zebra fish (Danio rerio) may serve as a model for elucidation of these inadequately understood mechanisms. Two hapten-mediated IBD-like models in zebra fish have been generated by using the chemicals oxazolone and TNBS dissolved in ethanol. From mammalian models it is known that oxazolone and TNBS can induce conditions mimicking ulcerative colitis (Th2 like response) and Crohn's disease (Th1/Th17 like response), respectively. Zebra fish (body weight 0.5 g) were divided into 4 groups (each with 2 replicates) and instilled rectally with H2O, ethanol, TNBS or oxazolone. Samples (intestine) were taken for realtime quantitative PCR. An array of TagMan assays was designed using Primer3Plus. All assays were checked by melting curve analysis in SYBR Green and by 3% agarose gel electrophoresis in order to ensure specificity. The assays include transcription factors and cytokines of different subsets of T-cell populations, cell markers etc. The 2-Ct method was used to estimate the fold change of gene expression relative to the H2O instilled group. Only results with p>0.05 and regulations >2 are discussed. The solvent ethanol, necessary for dissolving oxazolone and TNBS, itself up-regulates genes (T-bet, INF, IL-17A, TGF) primarily from the Th1/Th17 response but also IL-10 of the Th2 response. The gene expression pattern of the oxazolone and TNBS instilled groups were partly similar pointing primarily towards a Th2 response. TNF was the only Th1response specific gene up-regulated. In both groups the expression of 2 typically IBD markers IL-8 and Mmp9 were up-regulated whereas Myd88 seemed unaffected. In conclusion, as judged by the gene expression analysis the zebra fish could serve as a general model for IBD, although the presented results cannot distinguish between ulcerative colitis and Crohn's disease.