OBJECTIVES: Markov models developed for cost-effectiveness analysis (CEAs) often contain differences in model structure due to differences in assumptions. Such differences may lead to differences in outcome and can therefore impact decision making. The objective of this analysis was to identify structural assumptions, reported for CEAs comparing the cost-effectiveness of tamoxifen and anastrazole for adjuvant breast cancer therapy, and to subsequently evaluate the impact of these assumptions, both individually as well as combined, on analysis outcome measures. METHODS: Based on a literature review of available published Markov model based CEAs comparing tamoxifen and anastrazole, structural model assumptions were identified. Subsequently, a base case model was defined and built in R, representing the fundamental structure present in all identified CEAs from literature. Subsequently, different structural model components as identified from the published CEAs, were added to the base case model separately, as well as simultaneously. Outcome measures Life Years gained (LYG) and incremental costs were calculated for each of these models. RESULTS: The base case model outcome demonstrated a gain of 0.263 LYG for anastrazole compared to tamoxifen with an ICER of €13.868/LYG. The separate impact of assumptions on LYG, ranged from 0.207 to 0.356, while ICERs ranged from €9804/LYG to €17.966/LYG. For the comparison of combined assumptions as present in identified CEA’s, LYs gained ranged even from 0.207 to 0.383 with ICERs ranging from €9683/LYG to €17.570/LYG. CONCLUSIONS: It was possible to develop a unique base case Markov model for early breast cancer from the literature and to adjust this model taking various published assumptions into account. The adaptation of various assumptions resulted in differences in outcomes of CEAs of adjuvant breast cancer therapies. This case example demonstrates the importance of the development of standardized model structures for adjuvant breast cancer therapies.