A mitochondrial DNA deletion in a case of Kearns-Sayre syndrome is described. The deletion is bracketed by direct repeats that were unusual in that one of them was located 11-13 nucleotides from the deletion seam and both were conserved, which should not occur in slip replication or illegitimate elongation. The deleted region was demarcated on the deletion side by sequences that could be predicted to form hairpin structures. The 5'-side of the deletion was flanked by a sequence homologous to a 9-nucleotide piece of the conserved sequence block II of the D-loop. This arrangement around the deletion in Kearns-Sayre syndrome bears some resemblance to the arrangement in the Pearson marrow-pancreas syndrome described by A. Rötig et al. (1991, Genomics 10: 502-504).