Induced pluripotent stem cell (iPSC) line was derived from peripheral blood mononuclear cells (PBMCs) of a Kearns-Sayre syndrome (KSS) patient with mtDNA deletion of 4.8 kilobase fragment. KSS is an ultrarare multi-organ disorder and is characterized with (1.1 to 10 kilobase) deletion of mitochondrial DNA (mtDNA) with a frequency of ~1 in 100,000 individuals. Heteroplasmy in PBMCs allowed us to generate an iPSC line with normal mitochondrial DNA that can be used to study therapeutic prospective of iPSC and their derivatives and design future cell replacement therapies.