Abstract Objective Variation in emergency department head computed tomography (CT) use in patients with atraumatic headaches between hospitals is being measured nationwide. However, the magnitude of interphysician variation within a hospital is currently unknown. We hypothesized that there was significant variation in the rates of physician head CT use, both overall and for patients diagnosed with atraumatic headaches. Methods This cross-sectional study was conducted in the emergency department of a large urban academic hospital, and institutional review board approval was obtained. All emergency department visits from 2009 were analyzed, and the primary outcome measure was whether or not head CT was performed. Logistic regression was used to control for patient, physician, and visit characteristics potentially associated with head CT ordering. The degree of interphysician variability was tested, both before and after controlling for these variables. Results Of 55,286 emergency department patient encounters, 4919 (8.9%) involved head CT examinations. Unadjusted head CT ordering rates per physician ranged from 4.4% to 16.9% overall and from 15.2% to 61.7% in patients diagnosed with atraumatic headaches, with both rates varying significantly between physicians. Two-fold variation in head CT ordering overall (6.5%-13.5%) and approximately 3-fold variation in head CT ordering for atraumatic headaches (21.2%-60.1%) persisted even after controlling for pertinent variables. Conclusion Emergency physicians vary significantly in their use of head CT both overall and in patients with atraumatic headaches. Further studies are needed to identify strategies to reduce interphysician variation in head CT use.