- Medication omissions and dosing failures are frequent during transitions in patient care. Medication reconciliation (MR) requires bridging discrepancies in a patient’s medical history as a setting for care changes. MR has been identified as vulnerable to failure, and a clinician’s cognition during MR remains poorly described in the literature. We sought to explore cognition in MR tasks. Specifically, we sought to explore how clinicians make sense of conditions and medications. We observed 24 anesthesia providers performing a card-sorting task to sort conditions and medications for a fictional patient. We analyzed the spatial properties of the data using statistical methods. Most of the participants (58%) arranged the medications along a straight line (p < 0.001). They sorted medications by organ systems (Friedman’s χ 2(54) = 325.7, p < 0.001). These arrangements described the clinical correspondence between each two medications (Wilcoxon W = 192.0, p < 0.001). A cluster analysis showed that the subjects matched conditions and medications related to the same organ system together (Wilcoxon W = 1917.0, p < 0.001). We conclude that the clinicians commonly arranged the information into two groups (conditions and medications) and assigned an internal order within these groups, according to organ systems. They also matched between conditions and medications according to similar criteria. These findings were also supported by verbal protocol analysis. The findings strengthen the argument that organ-based information is pivotal to a clinician’s cognition during MR. Understanding the strategies and heuristics, clinicians employ through the MR process may help to develop practices to promote patient safety.