Gene therapy is an emerging type of treatment that may aim to provide a cure to individuals with a genetic mutation known to be causative of a specific disease. A diagnosis of the causative mutation must precede treatment with a in vivo gene therapy. Both achieving a genomic-based diagnosis and treatment with a gene therapy may result in substantial expenditures for health care systems. Uncertainties around the health care costs, risks, and benefits derived from diagnosis and treatment with a subsequent gene therapy suggests a need for developing an evidence base, underpinned by opportunity cost, to inform if, and how, these health technologies should be introduced into health care systems funded by finite budgets. This article discusses why current methods to evaluate health technologies (decision-analytic model-based cost-effectiveness analysis from the perspective of a health care system over a lifetime time horizon) are appropriate to quantify the costs and consequences of using genomic-based diagnostic tests and gene therapies in combination, rather than as separate interventions, within clinical practice. Evaluating the economic impact of test-and-treatment strategies will ensure that the opportunity cost of these health technologies is quantified fully for decision-makers who are responsible for allocating limited resources in health care systems.