INTRODUCTION: Secure messaging is a relatively new addition to health information technology (IT). Several studies have examined the impact of secure messaging on (clinical) outcomes but very few studies have examined the impact on workflow in primary care clinics. In this study we examined the impact of secure messaging on workflow of clinicians, staff and patients. METHODS: We used a multiple case study design with multiple data collections methods (observation, interviews and survey). RESULTS: Results show that secure messaging has the potential to improve communication and information flow and the organization of work in primary care clinics, partly due to the possibility of asynchronous communication. However, secure messaging can also have a negative effect on communication and increase workload, especially if patients send messages that are not appropriate for the secure messaging medium (for example, messages that are too long, complex, ambiguous, or inappropriate). Results show that clinicians are ambivalent about secure messaging. Secure messaging can add to their workload, especially if there is high message volume, and currently they are not compensated for these activities. Staff is -especially compared to clinicians- relatively positive about secure messaging and patients are overall very satisfied with secure messaging. Finally, clinicians, staff and patients think that secure messaging can have a positive effect on quality of care and patient safety. CONCLUSION: Secure messaging is a tool that has the potential to improve communication and information flow. However, the potential of secure messaging to improve workflow is dependent on the way it is implemented and used.