Objectives (i) To document the current state of the English, Scottish, Welsh, Northern Irish and Australian bowel cancer screening programmes, according to seven key characteristics, and (ii) to explore the policy trade-offs resulting from inadequate funding. Setting United Kingdom and Australia. Methods A comparative case study design using document and key informant interview analysis. Data were collated for each national jurisdiction on seven key programme characteristics: screening frequency, population coverage, quality of test, programme model, quality of follow-up, quality of colonoscopy and quality of data collection. A list of optimal features for each of the seven characteristics was compiled, based on the FOBT screening literature and our detailed examination of each programme. Results Each country made different implementation choices or trade-offs intended to conserve costs and/or manage limited and expensive resources. The overall outcome of these trade-offs was probable lower programme effectiveness as a result of compromises such as reduced screening frequency, restricted target age range, the use of less accurate tests, the deliberate setting of low programme positivity rates or increased inconvenience to participants from re-testing. Conclusions Insufficient funding has forced programme administrators to make trade-offs that may undermine the potential net population benefits achieved in randomized controlled trials. Such policy compromise contravenes the principle of evidence-based practice which is dependent on adequate funding being made available.