BACKGROUND Understanding how patients move through outpatient clinics is important for optimizing clinic processes. This study compares the costs, benefits, and challenges of two clinically important methods for measuring patient flow: (1) a commercial system using infrared (IR) technology that passively tracks patient movements and (2) a custom-built, low cost, networked radio frequency identification (RFID) system that requires active swiping by patients at proximity card readers. METHODS Readers for both the IR and RFID systems were installed in the General Eye Service of the Wilmer Eye Institute. Participants were given both IR and RFID tags to measure the time they spent in various clinic stations. Simultaneously, investigators recorded the times at which patients moved between rooms. These measurements were considered the standard against which the other methods were compared. RESULTS One hundred twelve patients generated a total of 252 events over the course of 6 days. The proportion of events successfully recorded by the RFID system (83.7%) was significantly greater than that obtained with the IR system (75.4%, p < 0.001). The cause of the missing events using the IR method was found to be a signal interruption between the patient tags and the check-in desk receiver. Excluding those data, the IR system successfully recorded 94.4% of events (p = 0.002; OR = 3.83 compared to the RFID system). There was no statistical difference between the IR, RFID, and manual time measurements (p > 0.05 for all comparisons). CONCLUSIONS Both RFID and IR methods are effective at providing patient flow information. The custom-made RFID system was as accurate as IR and was installed at about 10% the cost. Given its significantly lower costs, the RFID option may be an appealing option for smaller clinics with more limited budgets.