The relationship between mitochondrial genotype and mitochondrial phenotype was investigated in lymphoblasts derived from a patient with the Pearson syndrome. In 70% of the mtDNA of this Pearson cell line a deletion from within the COX II gene to within the ND5 gene was present. The deletion led to a reduced expression of the deleted genes, but the severely lowered synthesis of e.g. subunit II of cytochrome c oxidase was not reflected in a significant decrease in the cytochrome c oxidase activity. Moreover, there were no obvious differences between control cells and Pearson cells regarding the capacity for oxidative phosphorylation. Analysis of the synthesis and assembly of both nuclearly and mitochondrially encoded subunits of cytochrome c oxidase showed that normally mtDNA-encoded polypeptides are produced in excess. This overproduction fully explained the discrepancy between the severe defect in the expression of the mitochondrial genome and the normal mitochondrial function in the Pearson cells. These data demonstrate that the expression of one or more mitochondrial genes can be reduced specifically at intermediate percentages of deleted mtDNA. However, the data also suggest that whether or not a lower expression of mitochondrial genes encoding subunits of enzymes involved in oxidative phosphorylation influences the normal function of these enzymes depends on the relative abundance of the mitochondrial subunits in tissues or cells with deleted mtDNA.