Myotonia congenita can be either an autosomal dominant or autosomal recessive disease. With the autosomal dominant form, a person only needs to inherit defective genes from one parent, while inheriting the recessive form requires defective genes from both parents. The gene that causes this condition resides on chromosome 7.

The cause of myotonia congenita is believed to be an abnormality in the muscle cells' chloride channels. (Chloride ions are required for a muscle to relax.) The abnormal chloride channels also cause an accumulation of potassium outside the cells and an activation of sodium channels in the muscle cells. (Sodium ions trigger muscle contraction.)

When the cells have more than enough sodium but not enough chloride, abnormal repetitive electrical discharges cause a stiffness called myotonia.