We report a 42-year-old male suffering from congenital nemaline myopathy accompanied with mitochondrial abnormalities in his muscle biopsy. He had a dysmorphic face with a high-arched and narrow palate and slowly progressive generalized muscle weakness. He was still able to walk with a cane. CT showed symmetrical muscle atrophy and low densities in the thigh muscles, especially in the posterior compartment, and in the soleus muscles. Preferential posterior thigh involvement was unusual in congenital nemaline myopathy. The lumbar quadrate and paravertebral muscles were relatively well preserved; these muscles were reported to be severely involved in adult-onset nemaline myopathy patients. Muscle biopsy findings were consistent with nemaline myopathy; nemaline rods in approximately 10% of fibers, type 1 fiber atrophy, and type 2B fiber deficiency. In addition, ragged-red fibers were scattered and focal cytochrome c oxidase (CCO) deficiency was present. Formazan granules were large on succinate dehydrogenase stain. Many fibers with nemaline rods showed focal CCO deficiency. On electron microscopy, large (megaconial) mitochondria were lined regularly between Z lines. PCR and Southern blot analysis of muscle mitochondrial DNA revealed multiple deletions. It remains to be clarified whether mitochondrial abnormalities are primarily related to nemaline myopathy or secondarily induced phenomenon after a long-standing disease process.