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Chitosan-modified magnetic nanoparticles are a promising basis for the creation of new diagnostic agents and therapeutic drugs. The cells of erythroid, granulocytic, monocytic, lymphocytic, and megakaryocytic lineages of bone marrow of mature rats were investigated for 120 days after single injection of 0.14 g per 1 kg body weight chitosan-modified magnetic nanoparticles (Fe3O4). Light microscopy was applied to describe the structure of hematopoietic cells and morphometric study was performed on Romanowsky—Giemsa stained smears to measure cells size (µm) and relative number (%). Comparison of the biological effects of nonmodified and modified magnetite nanoparticles on hematopoietic cells of bone marrow revealed the advantages of modification. Chitosan-modified magnetite nanoparticles did not affect the structure of hematopoietic cells in the rat bone marrow, and their injection produced a reversible increase in the relative number of monocytes, stab neutrophils and segmented neutrophils, as well as polychromatic and oxyphilic normoblasts.