Previous studies of cytochrome c oxidase (complex IV of the respiratory chain) in the heart of a 26-year-old man with longstanding Kearns-Sayre syndrome and fatal congestive cardiomyopathy had revealed the presence of randomly distributed enzyme-deficient cardiomyocytes, both in the contractile and the conducting myocardium. In the present study, the conduction system of the heart was screened for the occurrence of the common 4977 base pair deletion (8, 482-13, 459) of mitochondrial DNA (mtDNA) in formalin-fixed, paraffin-embedded tissue and compared with the contractile myocardium. Polymerase chain reaction analysis revealed that in the sinus node, the atrioventricular node, and the bundle branches, 35 to 40% of total mtDNA molecules harbored the common deletion. In contrast, in the contractile myocardium, 10 to 20% of total mtDNA was deleted (P = .05). These results demonstrate that in Kearns-Sayre syndrome, the conduction system of the heart preferentially accumulates the common deletion. This finding might help to explain the high prevalence of cardiac dysrhythmias in this syndrome.