To establish a noninvasive genetic diagnosing method for Kearns-Sayre syndrome, the authors used the polymerase chain reaction (PCR) technique for detecting mitochondrial DNA (mtDNA) deletions in the platelets and directly sequenced the crossover regions of the deleted mtDNA using the fluorescence-based automated sequencing system. The mtDNA deletions were identified in the platelets of three of four patients. The sizes and locations of deletions were determined by the nesting primer PCR method, in which the primary PCR products derived from deleted mtDNAs undergo reamplification using a series of nesting primers. With the fluorescence-based sequencing of templates amplified by the asymmetric PCR method, deleted mtDNA was sequenced directly without cloning. In patient 1, guanine (G) was found at the boundaries of a deleted segment spanning 8400 base pairs (bp) between the CO1 and ND6 genes. In patient 2, a 9-bp directly repeated sequence of 5'-ACCTCCCTC-3' (where A = adenine, C = cytosine, and T = thymine) was found at the boundaries of a deleted segment spanning 7221 bp between the CO1 and ND5 genes. In patient 3, an 8-bp sequence of 5'-TCGCTGTC-3' was found at the boundaries of a deleted segment spanning 4664 bp between the ATPase6 and ND5 genes. Deletions were not detected in the mtDNA of patient 4 or in that of the mothers of the patients. Previously, the genetic diagnosis of this syndrome required muscle biopsy specimens and the use of Southern blot analysis. However, this method requires neither muscle biopsy nor isotopes and is more rapid than the Southern blot method.(ABSTRACT TRUNCATED AT 250 WORDS)