Among 40 patients with ragged red fibers in muscle biopsy, all but two met criteria for one of the recognized mitochondrial myopathies: Kearns-Sayre syndrome (6 patients); other ophthalmoplegias (17): MELAS (3); MERRF (2); limb myopathy (5); and exercise intolerance (3). Two patients had MNGIE (mitochondrial myopathy with neuropathy, gastrointestinal symptoms and encephalopathy) and one had spinal muscular atrophy. The myopathy had features of facioscapulohumeral dystrophy in 4 patients. This analysis provides 4 lines of evidence to reinforce the view that, despite occasional "overlap" cases, distinct syndromes can be recognized. First, there are clinical differences. Second, KSS is almost never familial but MELAS and MERRF are often familial. Third, in this series, as in others, all deletions of mtDNA were found in patients with either KSS or non-familial PEO. With a possible single exception, none of the familial cases had KSS and no familial cases included a deletion of mtDNA. Others have found evidence of mtDNA point mutations in MERRF, and maternal inheritance suggests that point mutations will be found in MELAS. Finally, postmortem findings differ in KSS, MELAS, and MERRF. For all of these reasons, we believe it is useful to separate cases on clinical grounds. Deletions and point mutations of mtDNA are becoming defining characteristics of these syndromes.