BACKGROUND: Accounting for preference heterogeneity is a growing analytical practice in health-related discrete choice experiments (DCEs). As heterogeneity may be examined from different stakeholder perspectives with different methods, identifying the breadth of these methodological approaches and understanding the differences are major steps to provide guidance on good research practices. OBJECTIVES: Our objective was to systematically summarize current practices that account for preference heterogeneity based on the published DCEs related to healthcare. METHODS: This systematic review is part of the project led by the Professional Society for Health Economics and Outcomes Research (ISPOR) health preference research special interest group. The systematic review conducted systematic searches on the PubMed, OVID, and Web of Science databases, as well as on two recently published reviews, to identify articles. The review included health-related DCE articles published between 1 January 2000 and 30 March 2020. All the included articles also presented evidence on preference heterogeneity analysis based on either explained or unexplained factors or both. RESULTS: Overall, 342 of the 2202 (16%) articles met the inclusion/exclusion criteria for extraction. The trend showed that analyses of preference heterogeneity increased substantially after 2010 and that such analyses mainly examined heterogeneity due to observable or unobservable factors in individual characteristics. Heterogeneity through observable differences (i.e., explained heterogeneity) is identified among 131 (40%) of the 342 articles and included one or more interactions between an attribute variable and an observable characteristic of the respondent. To capture unobserved heterogeneity (i.e., unexplained heterogeneity), the studies largely estimated either a mixed logit (n = 205, 60%) or a latent-class logit (n = 112, 32.7%) model. Few studies (n = 38, 11%) explored scale heterogeneity or heteroskedasticity. CONCLUSIONS: Providing preference heterogeneity evidence in health-related DCEs has been found as an increasingly used practice among researchers. In recent studies, controlling for unexplained preference heterogeneity has been seen as a common practice rather than explained ones (e.g., interactions), yet a lack of providing methodological details has been observed in many studies that might impact the quality of analysis. As heterogeneity can be assessed from different stakeholder perspectives with different methods, researchers should become more technically pronounced to increase confidence in the results and improve the ability of decision makers to act on the preference evidence.