Inflammatory bowel disease (IBD) represents a complex spectrum of gastrointestinal diseases. Incorporating Crohn's disease (CD) and ulcerative colitis (UC), IBD is characterised by recurrent and chronic inflammation, significant morbidity, and an increasing global prevalence. Scientific advances regarding the aetiology, pathogenesis and treatment of these relapsing immune-mediated diseases have developed in parallel to the study of experimental models of intestinal inflammation. The correlation of phenotype, histology and immune response with mucosal gene expression, permits the investigation of induced pathology for human translation.Trichuris muris (mouse whipworm) infection induces chronic colitis in susceptible strains (e.g. AKR). Chronic disease displays both a polarised CD4+ T-helper1 (TH1) immune response and histological, transmural colonic inflammation. Conversely, resistant mouse strains (e.g. BALB/c) exhibit transient infection and inflammation which quickly resolves under a presiding TH2 response. Work presented in this thesis investigates differential gene expression and biological pathways central to colonic outcome, and the genetic basis of chronic T. muris-induced colitis.This thesis demonstrates that the phenotypic and transcriptional profile of the T. muris model shared many similarities to widely used experimental models of colonic inflammation and to human IBD. Mice susceptible to chronic colonic inflammation displayed functional gene expression differences to those of resistant mice, including the up-regulation of pro-inflammatory, apoptosis and chemokine signalling pathway genes. Cellular homeostasis pathways and tight junction molecules were conversely down-regulated. Infected AKR demonstrated predominant TH1/ TH17 transcriptional activity, presenting this model as a platform to examine biological commonalities among chronic colitides. A Quantitative Trait Locus (QTL) study, performed by crossbreeding resistant and susceptible strains to T. muris infection, then identified key autosomal loci linked to chronic disease. Genes associated with known biological pathways, differential gene expression, and parental strain single nucleotide polymorphisms provided a novel and powerful strategy to reduce the number of candidate genes for further analysis. Of 7 T. muris (TM) QTL identified, 3 displayed overlap with other murine studies of parasite susceptibility. A separate locus, TM3, demonstrated overlap with published QTL in 3 unrelated experimental models of colitis and overlaid the Cdcs1 locus. TM3 possessed 33 significantly transcribed polymorphic genes (e.g. Ptpn22, Fcgr1, Rorc, Vcam1 and Vav3). Phenotypic pathway analysis, text mining and time-course qPCR all highlighted Vav3 (Human 1p13.3, murine Chr3 101.9 MB) as a key biological candidate in colitis susceptibility. As a final test of relevance to human disease, clinically proven IBD medications were administered to AKR mice post-T. muris infection, at a time-point when chronic disease was well established. Anti-TNFalpha Ab and corticosteroid therapy were shown to suppress TH1-driven experimental colitis, without affecting parasitic infection. Additionally, anti-TNFalpha Ab treatment was found to reduce pro-inflammatory macrophages yet preserve regulatory alternatively activated macrophage numbers within the colon. A previously unreported finding.Sharing biological commonalities with human CD, Trichuris muris colitis represents an advanced and tractable murine model for understanding the pathobiological mechanisms of chronic inflammatory disease. The key facet of this model is that despite identical injury some inbred mouse strains develop chronic colitis whilst others recover quickly and fully. The identification of differential mechanisms which govern outcome and a new platform to investigate novel targets of disease and disease therapy has implications for gastrointestinal inflammatory diseases and mucosal immunology.