Differential diagnosis of congenital myotonia includes disorders in which myotonia is the main symptom, and that are periodical paralyses, myotonic dystrophy and myotonias caused my drugs. Congenital myotonia can be distinguished from these disordes by:

• Factors that provoke/ameliorate myotonia
• Presence of symptoms outside skeletal system
• Electromyographic testing

Myotonic dystrophy type 1 and 2 should always be considered in the differential diagnosis of myotonia congenita. Although some degree of muscular weakness and wasting may be observed in autosomal recessive myotonia congenita, the pattern of muscle weakness is very different and extramuscular manifestations including early cataracts, abnormal cardiac conduction, or endocrine dysfunction found in DM1 and DM2 are not observed in myotonia congenita. Dystorphic myotonias are caused by mutations in DMPK1 and ZNF9 genes and are inherited in autosomal-dominant fashion.