Comparing emissions scenarios is an essential part of mitigation analysis, as climate targets can be met in various ways with different economic, energy system and co-benefit implications. Typically, a central ‘reference scenario’ acts as a point of comparison, and often this has been a no policy baseline with no explicit mitigative action taken. The use of such baselines is under increasing scrutiny, raising a wider question around the appropriate use of reference scenarios in mitigation analysis. In this Perspective, we assess three critical issues relevant to the use of reference scenarios, demonstrating how different policy contexts merit the use of different scenarios. We provide recommendations to the modelling community on best practice in the creation, use and communication of reference scenarios.