Because of the diversity of clinical symptoms, the diagnosis of mitochondrial DNA (mtDNA) deletion disorders can be difficult. Here, we describe an 8-month-old boy presenting clinically exclusively with refractory anemia. Mutation analysis in our patient revealed a large, novel deletion in his mtDNA encompassing ATPase 6, cytochrome oxidase subunit III, NADH dehydrogenase genes ND3 to ND6, and cytochrome b. Comparison with other cases from the literature showed that there is no genotype-phenotype correlation regarding hematologic features. It is not possible to predict whether our patient will develop additional features from Pearson syndrome or Kearns-Sayre syndrome, both syndromic mitochondrial disorders with hematological manifestations.