Background <p>Next generation sequencing (NGS) can decrease the diagnostic odyssey for patients with rare diseases. However, valuing the combination of health and non-health outcomes associated with NGS is challenging. While stated preference methods can be used for monetary valuation of outcomes, frameworks that jointly account for both costs and benefits to determine cost-acceptability are limited. Insights into cost-acceptability can help inform pricing and access decisions where competition among NGS alternatives is imperfect or diagnostics are provided as a public good.</p> Methods <p>We used stated preference data to estimate the cost-acceptability of exome sequencing (ES) (i.e., cost at which ES provides value and users are willing-to-pay) in a user-based valuation. We estimated the benefit of ES as an alternative to all other diagnostic tests using a compensating variation model. Based on estimated net-benefit, we determined the proportion of users with positive expected net-benefit for varying cost (CAD$0-$15,000) and chance of diagnosis (10%-90%). We created a cost-acceptability frontier of costs and chance of diagnosis for a range of scenarios. Expected net-benefit and cost-acceptability were estimated for low-cost (CAD$1,600) and high-cost (CAD$11,660) ES scenarios.</p> Results <p>We find that at least half of users consider costs of up to CAD$10,000 acceptable if the chance of obtaining a diagnosis of ES is at least 50%. However, at least some users are willing to accept a chance of diagnosis below 50%, even if the associated cost are high.</p> Conclusion <p>Our proposed valuation framework suggests that many potential users of ES are willing to accept various combinations of cost and chance of diagnosis. Cost-acceptability is especially high if the chance of diagnosis is larger the 50%.</p>