Heteroplasmic mutations of mitochondrial DNA (mtDNA) are an important source of human diseases. The mechanisms governing transmission, segregation and complementation of heteroplasmic mtDNA-mutations are unknown but depend on the nature and dynamics of the mitochondrial compartment as well as on the intramitochondrial organization and mobility of mtDNA. We show that mtDNA of human primary and immortal cells is organized in several hundreds of nucleoids that contain a mean of 2-8 mtDNA-molecules each. Nucleoids are enriched in mitochondrial transcription factor A and distributed throughout the entire mitochondrial compartment. Using cell fusion experiments, we demonstrate that nucleoids and respiratory complexes are mobile and diffuse efficiently into mitochondria previously devoid of mtDNA. In contrast, nucleoid-mobility was lower within mitochondria of mtDNA-containing cells, as differently labeled mtDNA-molecules remained spatially segregated in a significant fraction (37%) of the polykaryons. These results show that fusion-mediated exchange and intramitochondrial mobility of endogenous mitochondrial components are not rate-limiting for intermitochondrial complementation but can contribute to the segregation of mtDNA molecules and of mtDNA mutations during cell growth and division.