OBJECTIVES: If multiple diagnostic modalities are available, an insurmountable number of strategies have to be compared to determine the most efficient one. Our aim is to develop a multistage decision analytic model to decide upon the most cost-effective diagnostic strategy to guide the treatment of faecal incontinence by physiotherapy and surgical anal sphincter repair. METHODS: Incremental cost-effectiveness analysis of diagnostic strategies, each including one to seven diagnostic modalities, five of which consist of two or three subtests. The primary endpoint is the success of physiotherapy or, in case of failure, the success of subsequent operative anal sphincter repair. An informed choice was made for a restricted set of strategies eligible for economic evaluation and modelling, based on methodological papers and on expert opinion on patient logistics. RESULTS: In theory, 8,41E+13 possible decisions have to be evaluated for each therapy. This number can be reduced to 1,063,859, if the most cost-effective subtest combination within each diagnostic modality is determined beforehand. This is very likely the most informative combination, for the cost differences are minimal. Next, four modalities make up an inseparable diagnostic test array from the patients’ logistics point of view. Within this array individual tests may be omitted and the order of tests is redundant. The array further reduces the number of decisions to be evaluated to 777. CONCLUSIONS: The number of possible diagnostic strategies can be succesfully reduced to manageable proportions through an evaluation of subtest combinations first and by taking into account patients’ logistics.