Smartphone use is rampant in everyday life and is increasing in: patient management, teaching and learning of medicine and health research. There is untapped potential to use smartphones as research tools in MER for a range of research approaches. Qualitative research is increasingly common in medical education research (MER). Smartphone use as a research tool has not been well explored in MER and this Guide will be useful to researchers considering integrating smartphones specifically in qualitative MER. First, we discuss the potential for smartphones in qualitative MER. Then, we discuss the opportunities and drawbacks for using smartphones in qualitative MER. We then provide three principles to consider when conducting smartphone MER: communication, ethics and reflection. Next we share ten lessons that emerged from the literature and our experiences. We end by looking to the future of smartphones in qualitative MER and hope this Guide provides evidence-based information to optimise smartphone use in qualitative MER. This Guide is important as there is an urgent need to redefine ethical boundaries to account for blurred lines between personal and professional use of smartphones.