During the past decade, outstanding progress in the areas of congenital and limb-girdle muscular dystrophies has led to staggering clinical and genetic complexity. With the identification of an increasing number of genetic defects, individual entities have come into sharper focus and new pathogenic mechanisms for muscular dystrophies, like defects of posttranslational O-linked glycosylation, have been discovered. At the same time, this progress blurs the traditional boundaries between the categories of congenital and limb-girdle muscular dystrophies, as well as between limb-girdle muscular dystrophies and other clinical entities, as mutations in genes such as fukutin-related protein, dysferlin, caveolin-3 and lamin A/C can cause a striking variety of phenotypes. We reviewed the different groups of proteins currently recognized as being involved in congenital and limb-girdle muscular dystrophies, associated them with the clinical phenotypes, and determined some clinical and molecular clues that are helpful in the diagnostic approach to these patients.