Eye tracking has become increasingly applied in medical education research for studying the cognitive processes that occur during the performance of a task, such as image interpretation and surgical skills development. However, analysis and interpretation of the large amount of data obtained by eye tracking can be confusing. In this article, our intention is to clarify the analysis and interpretation of the data obtained from eye tracking. Understanding the relationship between eye tracking metrics (such as gaze, pupil and blink rate) and cognitive processes (such as visual attention, perception, memory and cognitive workload) is essential. The importance of calibration and how the limitations of eye tracking can be overcome is also highlighted.