The important role of mitochondria in the process of programmed cell death is widely accepted now. There is a set of nuclear-encoded mitochondrial proteins involved in this process. Apart from this, a mitochondrion contains its own genetic apparatus comprising mtDNA and replication, transcription, and translation systems. However, a mechanism of mitochondria genetic information realization under apoptosis-inducing conditions has been understood poorly. Here, using real-time PCR technique, the number of mitochondrial genes and their transcripts in mouse spleen cells after whole-body X-ray irradiation at the dosage of 10 Gy has been evaluated. During 5 h after the irradiation, nuclear DNA was subjected to fragmentation, whereas mtDNA remained intact. Moreover, in the course of time after irradiation the number of mtDNA copies increased threefold. The process of mtDNA transcription was more susceptible to irradiation: 1 h after exposure the number of ND2, ND4, and CYTB gene transcripts sharply decreased. At 24 and 72 h after irradiation, ND2 and ND4 transcripts recovered to the control values, while CYTB remained rather low; no significant decrease of ATP6 transcripts was observed within the whole period of observation. The difference in mRNA levels of genes transcribed under the control of the same promoter for mice to be grown both under normal conditions and after X-ray irradiation allows us to propose that there is a posttranscriptional mechanism which regulates expression of mitochondrial genes and provides different recovery rates for different mitochondrial transcripts during the development of apoptosis.