An estimated 5% of cases of first-episode psychosis are due to rare and sometimes reversible causes that can be identified through diagnostic investigations that are currently less common in psychiatry, e.g. lumbar puncture, specialised brain imaging and genetic testing. The current clinical practice of the use of such technologies, however, raises several challenging ethical questions. Drawing on our multidisciplinary perspective spanning psychiatry, neurology, philosophy, neuroscience, sociology and medical ethics from three countries, we identify emerging ethical issues in the diagnosis of rare causes of psychosis. We group challenges thus: (a) diagnostic justice, (b) moral responsibility and (c) unintended consequences of diagnostic work-up. Justice challenges surrounded the role of (a) 'luck', (b) social capital and (c) prior psychiatric diagnoses in determining access to work-up. Moral responsibility challenges surround the extent to which (a) clinicians are expected to know the red flags and work-up for rare or ultra-rare causes; and (b) those running health systems should enable knowledgeable clinicians to provide the requisite work-up. Challenges related to unintended consequences include the risk of pursuing work-up of rare causes to reinforce (a) psychiatric exceptionalism and (b) paternalistic decision-making that doesn't allow space for patient preferences. Finally, we reflect on unresolved issues and future directions.