Objectives To measure setup and intrafraction variability for intracranial targets during treatment of patients immobilized with a Brainlab, Inc. thermoplastic head mask using ExacTrac© imaging on the treatment unit. Patients and Methods Between November 2007 and June 2008, 12 patients were treated with cranial fractionated stereotactic radiation therapy for 25–28 fractions. Patient offset was calculated by the ExacTrac© algorithm from the planning computed tomography and orthogonal kV images taken at the time of treatment. Shifts of the patient position were done when the initial offset was greater than 1.5 mm. If a shift was made, post-shift images were acquired before treatment. Images were also acquired post-treatment to determine intrafraction movement. Results A total of 849 pairs of images were obtained. The averaged results of all 12 patients were: setup offset was 1.98 mm, treatment offset was 0.57 mm, and post-treatment offset was 0.66 mm. Of 303 fractions treated, 30 fractions had a post-treatment offset greater than 1.5 mm. Conclusion Quantitative analysis of the data set including variability in patient setup and intrafraction motion shows patient position can be reproduced within 1.0 mm using Brainlab thermoplastic head mask systems using the ExacTrac© system.