OBJECTIVES: Genomic testing is becoming routine practice for diagnosing rare childhood diseases across many jurisdictions. The economic evidence underlying these implementation decisions is highly uncertain and focuses on intermediate endpoints that do not align with best practice guidelines, namely diagnostic yield. We sought to determine whether the current evidence base reflects parents’ values for the clinical implementation of genomic testing to diagnose rare childhood diseases. METHODS: We conducted 4 focus groups with parents in Vancouver,Canada and Oxford, United Kingdom, applying maximum variation sampling to capture a diversity of perspectives. Recruitment continued until two trained qualitative researchers agreed that thematic saturation was reached. Transcripts were analysed using a constant comparative technique. RESULTS: Thirty-three parents participated across the focus groups. Parents discussed a range of hopes and expectations related to the process of genomic testing, as well as the care and decision-making trajectory that would follow. Participants valued obtaining an etiologic diagnosis alongside process attributes such as diagnostic accuracy and wait times, as well as downstream expectations of testing. Alongside diagnostic accuracy, parents expected access to effective treatments, lifestyle modifications and genetic counselling services. Further considerations included genomic data security and the conditions under which data would be shared for research. Hypothetical willingness to pay for testing was contingent on illness severity, test accuracy, and the probability that testing would increase quality and/or length of life. CONCLUSIONS: Publicly funded health systems are responsible for ensuring that resource allocation decisions are responsive to available evidence and end user values. As demonstrated by this investigation, diagnostic yield fails to capture all valued outcomes relating to the clinical implementation of genomic testing for rare childhood diseases. Future economic evaluations of genomic testing that integrate health and non-health outcomes are necessary to meet public demand and ensure consistency with best practices.