Muscle biopsy is an invasive procedure consisting in the removal of skeletal muscle tissue, sometimes of the fascia, for histological and sometimes biochemical and molecular examinations. The indications are suspicions of myopathy, vasculitis and fasciitis. The diagnosis of muscle tumors is not cover in this review. If the procedure is relatively simple, the diagnostic efficient depends on the quality of the indication, the choice of muscle, the tissue preparation technique and the pathological analysis guided by clinical and paraclinical data. These elements require peculiar clinical, technical and histopathological expertises. For these reasons, muscle biopsy must be carried out in an expert center in this field. Open muscle biopsy is the most common technique in France. Bergström needle biopsies and conchotome are sometimes used. The preparation of the sample, after the biopsy and before its pathological analysis, involves the freezing of a fragment in isopenthane, the inclusion of a fragment in paraffin and the inclusion of a fragment in glutaraldehyde. Pathological examination includes the study of standard stains, histoenzymology, immunostaining and sometimes electron microscopy. Sample preparation for biochemistry and molecular biology studies requires its direct freezing in nitrogen or dry ice. The collection of an informed and signed consent by the patient is necessary for the realization of genetic analyzes and for the conservation of the remaining tissue in a center of biological resource approved by the National Commission of computing and freedoms (CNIL). Some of these techniques are systematic and others are guided by clinical suspicion.