Objective Patient preferences can be informative for health technology assessment (HTA) and payer decision making. However, applications may be different per country. The aim of this study therefore was to investigate HTA representatives' opinions on whether and how to incorporate patient preferences in HTA in their respective countries. Methods Three country-specific focus groups were conducted with three to seven HTA representatives from Germany, Belgium, and Canada. A predefined focus group guide was used that covered topics relating to how patient preferences can be used in HTA, namely HTA stage, weight, impact, and quality, as well as a case example of gene therapy. Transcripts were analyzed using NVivo 12 following thematic analysis. Results Across all HTA bodies, an interest in the use of patient preferences was observed for scientific advice and value assessments, but not through incorporation in quality-adjusted life-years and multi-criteria decision analysis. HTA representatives found it difficult to determine the weight patient preferences may receive in decision making, but thought it could have an impact on payer decision making if the study is of acceptable quality. Conclusions In the near future it may be impossible to achieve structural integration of patient preferences with other evidence in HTA (e.g., in cost-effectiveness analysis), but HTA bodies are willing to incorporate patient preferences in other HTA sections as supportive evidence. To allow for that use, future work should focus on meeting HTA and payer needs when conducting patient preference studies and on education of HTA and payer representatives regarding these studies.