Analyses of morphological disparity have been used to characterise and investigate the evolution of variation in the anatomy, function, and ecology of organisms since the 1980s. While a diversity of methods have been employed, it is unclear whether they provide equivalent insights. Here we review the most commonly used approaches for characterising and analysing morphological disparity, all of which have associated limitations that, if ignored, can lead to misinterpretation. We propose best practice guidelines for disparity analyses, while noting that there can be no “one-size-fits-all” approach. The available tools should always be used in the context of a specific biological question that will determine data and method selection at every stage of the analysis.