A current ambition of research into motivation and emotion in teaching and learning is to investigate motivation and emotion in more holistic ways and to dive deeper into the dynamics of motivation and emotion processes in the classroom setting. Physiological measures have the potential to reach these goals by moving beyond between-person comparisons of habitual, often self-reported, levels of motivation and emotion. For a long time, tracking physiology was only possible in lab settings, which is problematic for studying authentic processes as they occur during teaching and learning. But recent technological innovations have enabled physiological measurement in ambulatory settings, such as the classroom. For many educational researchers interested in motivation and emotion, dealing with these measures can be challenging. This chapter provides a basic introduction to physiological measures in general and heart rate in particular. We also discuss the conceptual meaning of heart rate in studies on motivation and emotion. Furthermore, we present concrete tips for collecting heart rate data (i.e. study preparation, data cleaning, and data analyses). An important conclusion is that physiological measures open up some new aspects of human functioning to educational researchers and can complement (but not replace) behavioural and self-report measures of motivation and emotion.