Kearns-Sayre syndrome (KSS) is an ultrarare multi-organ disorder, with a frequency of ~1 in 100,000 individuals. KSS is characterized with (1.1-10 kilobase) deletion of a mitochondrial DNA (mtDNA). We created an induced pluripotent stem cell (iPSC) line from peripheral blood mononuclear cells (PBMCs) of a patient with mtDNA deletion of 7.3 kilobase fragment. Heteroplasmy in PBMCs provides a novel opportunity to generate iPSC with normal mitochondrial DNA that can be used to develop patient specific cell replacement therapies in future. Hence, this unique line was created to study phenotype and therapeutic prospective of iPSC and their derivatives.