The atomic nuclei of cosmic rays possessing a high kinetic energy pose a significant threat to living organisms outside the Earth’s magnetic field. However, surprisingly, a series of ground-based studies using progressive models of combined irradiation revealed positive effects of such rays in relation to the functions of the central nervous system. The molecular mechanism of this phenomenon remains unknown. We have previously proposed a hypothesis that the serotonergic system may be involved in the realization of these effects. This research investigates the content of a number of biomolecules participating in serotonergic neurotransmission in selected morphological brain structures of rats under combined (γ-rays and 12 C 6+ ) irradiation. The revealed increase in 5-HT 2a in the prefrontal cortex may be a key link in the mechanism responsible for enhancing cognitive functions under moderate doses of ionizing radiation.