At present, gold nanoparticles (GNPs) are widely used in biomedical applications such as cancer diagnostics and therapy. Accordingly, the potential toxicity hazards of these nanomaterials and human safety concerns are gaining significant attention. Here, we report the effects of prolonged peroral administration of GNPs with different sizes (2, 15 and 50 nm) on morphological changes in lymphoid organs and indicators of peripheral blood of laboratory animals. The experiment was conducted on 24 white mongrel male rats weighing 180–220 g, gold nanospheres sizes 2, 15 and 50 nm were administered orally for 15 days at a dosage of 190 μg/kg of animal body weight. The GNPs were conjugated with polyethylene glycol to increase their biocompatibility and bioavailability. The size-dependent decrease of the number of neutrophils and lymphocytes was noted in the study of peripheral blood, especially pronounced after administration of GNPs with size of 50 nm. The stimulation of myelocytic germ of hematopoiesis was recorded at morphological study of the bone marrow. The signs of strengthening of the processes of differentiation and maturation of cellular elements were found in lymph nodes, which were showed as the increasing number of immunoblasts and large lymphocytes. The quantitative changes of cellular component morphology of lymphoid organs due to activation of migration, proliferation and differentiation of immune cells indicate the presence of immunostimulation effect of GNPs.