Abstract Carbon dots (CDs) are easy-obtained nanoparticles with wide range of biological activity; however, their toxicity after prolonged exposure is poorly investigated. So, in vitro and in vivo toxicity of CDs with the surfaces enriched with hydroxylated hydrocarbon chains and methylene groups (CD_GE), carboxyl and phenol groups accompanied with nitrogen (CD_3011), trifluoromethyl (CDF19) or toluidine and aniline groups (CDN19) were aimed to be discovered. CDs’ in vitro toxicity was assessed on A549 cells (real-time cell analysis of impedance, fluorescence microscopy) after 24 h of incubation, and we observed no changes in cell viability and morphology. CDs’ in vivo toxicity was assessed on C57Bl6 mice after multiple dosages (5 mg/kg subcutaneously) for 14 days. Lethality (up to 50%) was observed in CDN19 and CD_3011 groups on different days of dosing, accompanied by toxicity signs in case of CD_3011. There were no changes in serum biochemical parameters except Urea (increased in CDF19 and CD_3011 groups), nor substantial kidney, liver, and spleen injuries. The most impactful for all organs were also CD_3011 and CDF19, causing renal tubule injury and liver blood supply violation. Thus, CDs with a surface enriched with oxygen- and nitrogen-containing functional groups might be toxic after multiple everyday dosing, without, however, significant damages of internal organs in survived animals.