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Nano-particulate biomaterials have been used in clinical diagnosis and treatment, as drug carrier or in cosmetics because of their excellent performance properties. The toxicity and biocompatibility of nanoparticles (NPs), however, are always a focused concern for a doctor or a scientist. At present, there is almost no systemic evaluation standard or testing methods of safety for nanoparticles. In this study, two kinds of hydroxylapatite, (HAP) NPs with different particle sizes were selected. A number of biocompatibility tests in vivo or in vitro were conducted. They were cytotoxicity (MTT assay), genotoxicity (Ames, Mouse Lymphoma Mutagenesis Assay), and systemic toxicity (Acute and Subacute). The results indicated that, under the concentration of 100 mg/L, both HAP NPs could cause significant inhibition of cell growth. The size of NPs might have close tie with cell response. The mutagenic test in vitro was negative in this study. Histopathological findings showed that both kinds of HAP NPs could induce pseudotubercles in lung. Moreover, smaller size of nanoparticles resulted in a vacuolar degeneration of nephric tubule epithelium at 7 days post-intraveneous injection. The results implied that the size of NPs might play an important role in the biocompatibility of the materials. The kidney might be the main organ of discharge of nanoparticles from body.