Purpose Assessment in medical education has changed over time to measure the evolving skills required of current medical practice. Physical and biophysical markers of assessment attempt to use technology to gain insight into medical trainees’ knowledge, skills, and attitudes. The authors conducted a scoping review to map the literature on the use of physical and biophysical markers of assessment in medical training. Materials and methods The authors searched seven databases on 1 August 2022, for publications that utilized physical or biophysical markers in the assessment of medical trainees (medical students, residents, fellows, and synonymous terms used in other countries). Physical or biophysical markers included: heart rate and heart rate variability, visual tracking and attention, pupillometry, hand motion analysis, skin conductivity, salivary cortisol, functional magnetic resonance imaging (fMRI), and functional near-infrared spectroscopy (fNIRS). The authors mapped the relevant literature using Bloom’s taxonomy of knowledge, skills, and attitudes and extracted additional data including study design, study environment, and novice vs. expert differentiation from February to June 2023. Results Of 6,069 unique articles, 443 met inclusion criteria. The majority of studies assessed trainees using heart rate variability (n = 160, 36%) followed by visual attention (n = 143, 32%), hand motion analysis (n = 67, 15%), salivary cortisol (n = 67, 15%), fMRI (n = 29, 7%), skin conductivity (n = 26, 6%), fNIRs (n = 19, 4%), and pupillometry (n = 16, 4%). The majority of studies (n = 167, 38%) analyzed non-technical skills, followed by studies that analyzed technical skills (n = 155, 35%), knowledge (n = 114, 26%), and attitudinal skills (n = 61, 14%). 169 studies (38%) attempted to use physical or biophysical markers to differentiate between novice and expert. Conclusion This review provides a comprehensive description of the current use of physical and biophysical markers in medical education training, including the current technology and skills assessed. Additionally, while physical and biophysical markers have the potential to augment current assessment in medical education, there remains significant gaps in research surrounding reliability, validity, cost, practicality, and educational impact of implementing these markers of assessment.