Muscle biopsy is required to provide a definitive diagnosis in many neuromuscular disorders. Biopsy findings may indicate whether the pathological process is of neurogenic or myopathic origin. The muscle biopsy may give important information on the course of the disease (acute or chronic) and on the disease stage and progression. The interpretation of muscle biopsy, including histochemical and ultrastructural analysis, is a key factor in the diagnosis of muscular dystrophies, glycogenoses, inflammatory myopathies and congenital myopathies. An assessment of muscle biopsy on electron microscopy enables a definite diagnosis of oculopharyngeal muscular dystrophy, mitochondrial myopathy or inclusion body myositis. This paper presents an overview of general indications for muscle biopsy, biopsy procedures, as well as transportation and preparation of muscle tissue for final microscopic analysis. The interpretation of specific microscopic findings and a brief discussion on the clinical usefulness of muscle biopsy in the era of molecular diagnosis are also presented.