Knowledge of selective muscle-involvement is useful to the clinician. Therefore we investigated in sarcoglycanopathy and dysferlinopathy: (i) the correlation between clinical scale, MRC scale and CT findings and (ii) the muscles involved. Patients with a definite diagnosis of dysferlinopathy and sarcoglycanopathy were tested for their clinical functions and muscle strength and assigned a functional grade. Nineteen muscles were evaluated by CT. In dysferlinopathy, distal lower-limb muscles are involved, while in sarcoglycanopathy proximal muscles are more affected. In both groups, muscles with MRC < 3 often had severe abnormalities on CT imaging, while muscles with MRC > 4 could be either normal or abnormal. Dysferlinopathy and sarcoglycanopathy have different and selective muscle involvement. This may affect certain types of functional activity. There is a possible relationship between CT findings and MRC grade in muscles with a low (< 3) MRC grade. Abnormality on CT scan may precede the clinical symptoms.