Fatty infiltration in thigh skeletal muscle is a potential biomarker of osteoarthritis and post-traumatic osteoarthritis. Quantification of fatty infiltration is possible by Dixon MRI but is dependent on acquisition and processing. We evaluated five acquisition and processing techniques for reproducibility in phantom and healthy controls. Patients at 10-years post-ACL reconstruction were scanned to evaluate the potential for these techniques to detect thigh muscle fatty infiltration. Monopolar gradient acquisition and magnitude image-based processing improved the robustness of fat fraction quantification. Vendor-independent magnitude-based processing and vendor inline processing similarly quantified elevated fat fraction in the hamstring muscles of patients' ACL reconstructed legs.