OBJECTIVES: Crohn’s disease (CD) is a relapsing remitting inflammatory disease affecting the gastrointestinal tract. Previous economic evaluations in CD have focussed on single treatment comparisons within the treatment pathway. This project aimed to develop a model capturing lifetime costs and utilities throughout the entire treatment pathway. METHODS: A treatment sequence model was adapted from an earlier CD model by including the option to change treatments as patients stop responding. A Markov structure was used with five health-states: full-, partial- and no-response, surgery and death. Transition probabilities and survival rates were derived from previous analyses with separate transition matrices used for standard care and anti-TNF-αs. The model allows for ≤11 treatment stages (each with induction and maintenance phases) to be evaluated. Patients failing in induction progress to the next stage, if failing in maintenance they return to the induction treatment from that stage unless it is the same as the maintenance treatment. Surgery can be included as a separate treatment stage, although patients can receive surgery at any time. Costs were taken from published sources, and utilities from previous analyses. Limitations of available contemporary data and reporting of modelling methods posed challenges for model development; in particular the lack of data on the efficacy of combination treatment and probabilities of sustained response on anti-TNF-α therapies. RESULTS: In a patient cohort (mean age 35), lifetime costs and QALYs (LYs) were £169,560 and 14.85 (20.97) for a treatment pathway where patients initiated therapy with steroids + azathioprine followed by azathioprine maintenance, progressed through more intensive steroid induction, available anti-TNF-αs and surgery, ultimately becoming treatment refractory. CONCLUSIONS: This model represents an advance in economic evaluation of CD, allowing lifetime evaluation of treatment strategies in a complex treatment area. Further research into the natural history of CD would improve the potential for robust economic evaluation.