The fast pace of technological improvement and the rapid development and adoption of healthcare applications present crucial challenges for clinicians, users and policy makers. Some of the most pressing dilemmas include the need to ensure the safety of applications and establish their cost-effectiveness while engaging patients and users to optimize their integration into health decision-making. Healthcare organizations need to consider the risk of fragmenting clinical practice within the organization as a result of too many apps being developed or used, as well as mechanisms for app integration into the wider electronic health records through development of governance framework for their use. The impact of app use on the interactions between clinicians and patients needs to be explored, together with the skills required for both groups to benefit from the use of apps. Although healthcare and academic institutions should support the improvements offered by technological advances, they must strive to do so within robust governance frameworks, after sound evaluation of clinical outcomes and examination of potential unintended consequences.