Functional imaging might increase the role of imaging in muscular diseases, since alterations of muscle morphology alone are not specific for a particular disease. Perfusion, i.e., the blood flow per tissue and time unit including capillary flow, is an important functional parameter. Pathological changes of skeletal muscle perfusion can be found in various clinical conditions, such as degenerative or inflammatory myopathies or peripheral arterial occlusive disease. This article reviews the theoretical basics of functional radiological techniques for assessing skeletal muscle perfusion and focuses on contrast-enhanced ultrasound (CEUS) and magnetic resonance imaging (MRI) techniques. Also, the applications of microvascular imaging, such as in detection of myositis and for discriminating myositis from other myopathies or evaluating peripheral arterial occlusive disease, are presented, and possible clinical indications are discussed. In conclusion, dedicated MR and CEUS methods are now available that visualize and quantify (patho-)physiologic information about microcirculation within skeletal muscles in vivo and hence establish a useful diagnostic tool for muscular diseases.