Increasing numbers of healthcare professionals are using smartphones and their associated applications (apps) in daily clinical care. While these medical apps hold great potential for improving clinical practice, little is known about the possible dangers associated with their use. Breaches of patient confidentiality, conflicts of interests and malfunctioning clinical decision-making apps could all negatively impact on patient care. We propose several strategies to enhance the development of evidence-based medical apps while retaining their open nature. The increasing use of medical apps calls for broader discussion across medicine's organising and accrediting bodies. The field of medical apps is currently one of the most dynamic in medicine, with real potential to change the way evidence-based healthcare is delivered in the future. Establishing appropriate regulatory procedures will enable this potential to be fulfilled, while at all times ensuring the safety of the patient.