Mitochondrial DNA (mtDNA) deletions have been found in a majority of patients with Kearns-Sayre syndrome (KSS). The proband, a 14-year-old male, presented with retinitis pigmentosa, bilateral ptosis with an external opthalmoplegia, and ragged-red fibers in his biceps. The common 5-kb deleted mtDNA was identified in the patient by a long template PCR and DNA sequencing analysis. The deletion was located within the 8469-1344 position and a 13-kb direct repeat sequence was shown in the junction.