Computational phenotyping (CP) technology uses facial recognition algorithms to classify and potentially diagnose rare genetic disorders on the basis of digitised facial images. This AI technology has a number of research as well as clinical applications, such as supporting diagnostic decision-making. Using the example of CP, we examine stakeholders’ views of the benefits and costs of using AI as a diagnostic tool within the clinic. Through a series of in-depth interviews (n ​= ​20) with: clinicians, clinical researchers, data scientists, industry and support group representatives, we report stakeholder views regarding the adoption of this technology in a clinical setting. While most interviewees were supportive of employing CP as a diagnostic tool in some capacity we observed ambivalence around the potential for artificial intelligence to overcome diagnostic uncertainty in a clinical context. Thus, while there was widespread agreement amongst interviewees concerning the public benefits of AI assisted diagnosis, namely, its potential to increase diagnostic yield and enable faster more objective and accurate diagnoses by up skilling non specialists and thereby enabling access to diagnosis that is potentially lacking, interviewees also raised concerns about ensuring algorithmic reliability, expunging algorithmic bias and that the use of AI could result in deskilling the specialist clinical workforce. We conclude that, prior to widespread clinical implementation, on-going reflection is needed regarding the trade-offs required to determine acceptable levels of bias and conclude that diagnostic AI tools should only be employed as an assistive technology within the dysmorphology clinic.