Disorders of the rectus capitis posterior minor (RCPm) muscles have been associated with chronic headache. Magnetic resonance (MR) imaging protocols currently used in clinical settings do not result in image sets that can be used to adequately visualize the integrity of occipitoatlantal structures or to definitively quantify time-dependent functional morphologic changes. To develop an MR imaging protocol that provides the superior image quality needed to visualize occipitoatlantal soft tissue structures and quantify time-dependent pathologic changes. Asymptomatic participants were recruited from the Michigan State University College of Osteopathic Medicine student body. Magnetic resonance imaging data were collected from each participant at enrollment and 2 weeks after enrollment using a 3T magnet. A conventional spin-echo pulse sequence was used to construct 24 axial, T1-weighted images with the following measurement parameters: repetition time, 467 milliseconds; echo time, 13.5 milliseconds; number of excitations, 4; slice thickness, 3.0 mm; and in-plane resolution, 0.625×0.625 mm. Image planes were aligned approximately perpendicular to the long axes of the RCPm muscles to facilitate the authors' ability to accurately draw regions of interest around the specific muscle boundaries. Cross-sectional area (CSA) of the right and left RCPm muscles was quantified for each participant at the 2 points in time. The null hypothesis was that there would be no significant difference between mean values of muscle CSA collected at enrollment and 2 weeks after enrollment for a given participant and a given side of his or her body. Thirteen participants were enrolled. No significant difference was found between mean values of either right or left RCPm muscle CSA for any of the participants measured at enrollment and 2 weeks after enrollment (all P>.05). The protocol achieves the superior image quality necessary to compare the functional form of occipitoatlantal structures at progressive points in time.