Electronic medical records (EMRs) are changing the way physicians work and how medical staff care for patients. While their widespread adoption promise many benefits and computationally powerful features for end users, they may also carry with them other unintended and troubling consequences. As part of a larger ongoing research study, we deployed an unobtrusive eye tracker in outpatient clinics to observe how physicians use their EMRs. We report on our experiences and we derive a methodology for successful eye tracking data collection in the clinic. Our results highlight multiple applications for the quantitative and qualitative assessment of EMR interfaces from eye tracking data collected in situ. We describe one of these applications, the association of eye movements with the specific task that physicians engage with in the EMR, and we discuss both next steps and future application of these results.