Establishment of a comprehensive diagnostic system for patients with inherited myopathies is challenging because of their genetic heterogeneity. In this paper, we introduced our genetic diagnostic system using four target gene panels, each covering all exonic and flanking regions of genes associated with 1) muscular dystrophy, 2) congenital myopathy/congenital myasthenic syndrome, 3) metabolic myopathy, and 4) myopathy with protein aggregations/rimmed vacuoles, combined with comprehensive muscle histological, mRNA, and protein analyses. Our study indicates that targeted gene panels are cost- and time- effective and useful for screening pathogenic variants and for giving molecular diagnosis to the patients with inherited myopathies. (By Dr. Satomi Mitsuhashi, http://jmg.bmj.com/content/early/2016/09/06/jmedgenet-2016-104073 )