Myotilin is a muscle-specific Z disk protein. Several missense mutations in the myotilin gene (MYOT) have been identified in limb girdle muscular dystrophy (LGMD), myofibrillar myopathy, and distal myopathy patients. All previously reported pathogenic MYOT mutations have been identified only in Exon 2. We sequenced MYOT in 138 patients diagnosed as having LGMD, myofibrillar myopathy, or distal myopathy, and identified a novel MYOT mutation in Exon 9 encoding the second immunoglobulin-like domain in 1 patient with clinically typical LGMD. By light microscopy, there were scattered fibers with rimmed vacuoles and myofibrillary disorganization in the patient's muscle biopsy; accumulation of Z disk proteins was observed by immunohistochemistry. Immunoblot analysis demonstrated that the amount of myotilin monomer was increased in the patient muscle, but that the myotilin homodimeric band was decreased. Functional analysis of the myotilin mutation using a yeast 2-hybrid system revealed defective homodimerization of the mutant myotilin and decreased interaction between mutant myotilin and α-actinin. The homodimerization defect was further demonstrated by immunoprecipitation. This is the first MYOT mutation outside of Exon 2 in an LGMD type 1A patient and the first MYOT mutation identified in the Japanese population. This mutation in the second immunoglobulin-like domain impairs myotilin dimerization and alters the binding between myotilin and α-actinin, which is known to be important for actin bundling.