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The ability to make connections between physiological systems is a vital skill for undergraduate anatomy and physiology students. However, the literature is scarce with regard to what connections they make and the extent to which students make them. Using a mixed methods approach, we analyzed students’ (n = 21) talk from five collaborative online study groups at three times and identified the types of connections they made before/after a lesson that focused on generating connection questions. Qualitatively coded data revealed six categories of connections. We then employed an Epistemic Network Analysis to investigate the depth and dynamic movement of the patterns of the six types of connections over time. Notably, there was an increase in connection generation after the lesson.