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Health interventions should be tested before being introduced into clinical practice, to find out whether they work and whether they are harmful. However, research studies will only provide reliable answers to these questions if they are appropriately designed and analysed. But these are not trivial tasks. We review some methodological challenges that arise when evaluating fertility interventions and explain the implications for a non-statistical audience. These include flexibility in outcomes and analyses; use of surrogate outcomes instead of live birth; use of inappropriate denominators; evaluating cumulative outcomes and time to live birth; allowing each patient or couple to contribute to a research study more than once. We highlight recurring errors and present solutions. We conclude by highlighting the importance of collaboration between clinical and methodological experts, as well as people with experience of subfertility, for realising high-quality research.