Corneal clouding is uncommon in infants and children but when present in this age group, it is often associated with mucopolysaccharidoses or Fabry disease. This report describes the case of an 11-year-old male who demonstrated poor weight gain, short stature, segmental myoclonus, and learning problems from 5 years of age followed by general weakness and extremely poor balance. Corneal clouding was evident as a result of a blurred vision complaint at 9 years of age. Both urine metabolic screening for mucopolysaccharidoses and analysis of lysosomal enzymes displayed negative findings. Clinical conditions worsened, including ptosis, progressive weakness, and positive Gowers' sign. Oral glucose lactate stimulation test was positive, therefore a muscle biopsy was performed at 11 years of age. Light microscopy of muscle biopsy disclosed abundant ragged red fibers; electron microscopy revealed abnormal mitochondria in terms of tubular cristae, concentrated cristae, stacking cristae, and round granular patterns of inclusion bodies in the matrix. Thus mitochondrial disease was diagnosed. We conclude that mitochondrial disease should be added to the list of differential diagnosis of corneal clouding in children, especially in cases with normal urine metabolic screening for mucopolysaccharidoses or when assays of lysosomal enzymes appear normal.