Rise in the frequency of age-related diseases (neurodegenerative and cardiovascular diseases, osteoporosis, etc.) has great socio-economic implications. Great pathogenetic significance of age changes in functioning of the immune and neuroendocrine systems and their relationship with dysfunction of the central organs (thymus and pineal gland) has been established. On the contrary, melatonin and thymic hormones not only inhibit age changes in functioning of the above systems and diminish the incidence of age-related diseases but also improve their clinical results. Inhibiting effects of thymus and pineal gland factors on the development of age-related diseases can also be explained by their action on biological properties (proliferating and differential potential) of proper stem cells of different types in the organism organs. Noteworthy, the effect of melatonin on certain types of stem cells is realized not only directly but also indirectly via alteration of thymic endocrine function and functioning of endocrine glands. Thus, the pineal gland can provide adaptive (rhythmical) changes of the proliferative and differential potential of proper stem cells. Transplantation of different types of stem cells is used as stem therapy during already developed disorders. Nevertheless, at these diseases, the age-related dysfunction of the thymus and pineal gland is enhanced along with the changes in body organs interrelations. Therefore, therapeutic effects of stem cells transplantation can show themselves or be enhanced against the background of renewal of rhythmicity of pineal-thymus interactions. Maintenance of immune-endocrine interactions involving thymus and pineal gland plays role in the stem cell therapy of age-related diseases.