Background: Diagnostic ultrasound (US) offers a cost-effective and accessible means of evaluating the cross-sectional area (CSA) of muscles as compared to the gold standard of Magnetic Resonance Imaging (MRI). Muscle CSA is directly related to the amount of force a muscle can produce. Rotator cuff CSA is especially important when considering the strength and function of the shoulder joint. The present study aims to test the validity, same-day and between day intra-rater reliability of US CSA measures of the supraspinatus (SS) and infraspinatus (IS) muscles of the shoulder compared to MRI. Methods: Thirty-two, right-hand dominant subjects were prospectively enrolled and completed this study. A protocol was developed using previous research to measure the SS and IS CSA with US. US images were compared to corollary MRI images to test validity. Same-day intra-rater reliability was tested on all 32 subjects. Fourteen subjects were asked to return for follow up US imaging in order to test between-day intra-rater reliability. Twelve subjects with right shoulder pain referred for an MRI and 12 case-matched healthy controls were used to test criterion validity. Results: US demonstrated acceptable criterion validity when compared to MRI and acceptable same-day and between-day intra-rater reliability. Conclusion: This present study showed that US is a valid and reliable tool in measuring the CSA of the SS and IS muscles of the shoulder. Ultrasound CSA measures of the SS and IS muscles demonstrate acceptable criterion validity and same-day and between-day intra-rater reliability.