Mitochondria play a key role in a number of physiological events during all stages of life, including the very first stages following fertilization. It is, therefore, important to understand the mechanisms controlling mitochondrial activity during early embryogenesis to determine their role in development outcome. The objective of this study was to investigate the molecular control of mitochondrial transcription and mitochondrial DNA (mtDNA) replication in mouse preimplantation embryos. We estimated the mtDNA copy number and characterized the expression patterns of two mitochondrial genes and several nuclear genes that encode mitochondrial transcription and replication factors throughout preimplantation development. Mitochondrial gene transcripts were present in larger quantities in morula and blastocyst stage embryos relative to other stages. A significant increase in the amount of mRNA for nuclear genes encoding mtDNA transcription factors was observed in eight-cell stage embryos. Although a similar increase in the mRNA levels of nuclear genes encoding mtDNA replication factors was observed in morula and blastocyst stage embryos, the number of mtDNA molecules remained stable during preimplantation stages, suggesting that nuclear-encoded mitochondrial transcription factors are involved in the regulation of mtDNA transcription during early development. Although transcripts of replication factors are abundant at the morula and blastocyst stage, mtDNA replication did not occur until the blastocyst stage, suggesting that the inhibition of mtDNA replication is controlled at the post-transcriptional level during early embryogenesis.