We investigated the biological effects of selected nanomaterials that have potential for medical use. Effects of nanomaterials were evaluated on the canine kidney MDCK cells and on the human lung A549 cells with properties of alveolar type II cells. The main purpose of the doctoral work was to determine whether nanomaterials can induce phospholipidosis (excessive intracellular accumulation of phospholipids in lamellar bodies) as early sign of adverse effects of nanomaterials. In addition, we wanted to check if biological effects of nanomaterials depend on their size and on their dissolution. On MDCK cells that were exposed to sub-cytotoxic concentrations of ZnO nanoparticles, ZnO microparticles and to zinc salt ZnCl2, we observed increased DNA damage only in cells exposed to nanoparticles. By measuring the ZnO nanoparticle dissolution, we found that the zinc ion release in the cell culture medium is insufficient to be the main cause of ZnO nanoparticle toxicity. By staining cells with LipidTOX™ phospholipidosis dye that is used to test potential for phospholipidosis induction, we found that ZnO nanoparticles as well as all other selected nanomaterials did not increased the amount of phospholipid rich organelles in MDCK cells. In contrast, in A549 cells, we observed that silica coated maghemite nanoparticles (γ-Fe2O3+SiO2) caused increased cellular content of phospholipids rich organelles, increased content of phosphatidylcholine (PC) and increased content of organelles that are involved in lamellar body biogenesis. Despite these results, indicating intensive lamelar body biogenesis in the exposed A549 cells, the amount of lamellar bodies had been decreased. In γ-Fe2O3+SiO2 treated A549 cells, we observed an increased amount of autophagic vacuoles that often contained defective lamellar bodies destined for degradation. Results on A549 cells showed that γ-Fe2O3+SiO2 affect lipid metabolism, interfered with the lamellar body biogenesis and reduced cell capacity to lower the surface tension of hypophase. Our results show that phospholipidosis is not good indicator of nanotoxicity in MDCK and A549 cells. Nevertheless we have shown that nanomaterials can induce DNA damage and may interfere with important functions of the cell, even at non-cytotoxic concentrations.