A 26-year-old female with myoclonus epilepsy associated with ragged-red fibers is reported. Clinically, she had myoclonus epilepsy, cerebellar ataxia, a bilateral neurosensory type hearing loss, retinitis pigmentosa and short stature. She also presented with primary amenorrhea and poor development of secondary sexual characteristics. Endocrinologic studies revealed that hypothalamic dysfunction was the most plausible cause of her primary amenorrhea. Magnetic resonance imaging showed marked dilatation of the third ventricle indicating thalamic and hypothalamic degeneration. We conclude that hypothalamic dysfunction may be one of the characteristic features of mitochondrial encephalomyopathies.