Shear wave elastography (SWE) is a clinical ultrasound imaging modality that enables non-invasive estimation of tissue elasticity. However, various methodological factors—such as vendor-specific implementations of SWE, mechanical anisotropy of tissue, varying anatomical position of muscle and changes in elasticity due to passive muscle stretch—can confound muscle SWE measurements and increase their variability. A measurement protocol with a low variability of reference measurements in healthy subjects is desirable to facilitate diagnostic conclusions on an individual-patient level. Here, we present data from 52 healthy volunteers in the areas of: (1) Characterizing different limb and truncal muscles in terms of inter-subject variability of SWE measurements. Superficial muscles with little pennation, such as biceps brachii, exhibit the lowest variability whereas paravertebral muscles show the highest. (2) Comparing two protocols with different limb positioning in a trade-off between examination convenience and SWE measurement variability. Repositioning to achieve low passive extension of each muscle results in the lowest SWE variability. (3) Providing SWE shear wave velocity (SWV) reference values for a specific ultrasound machine/transducer setup (Canon Aplio i800, 18 MHz probe) for a number of muscles and two positioning protocols. We argue that methodological issues limit the current clinical applicability of muscle SWE.