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Nanomedicine and nano-delivery systems are a relatively new but rapidly developing science where nanoparticles (NPs) are employed to deliver therapeutic agents to specifically targeted sites in a controlled manner. Many of these NPs may have toxic effects on human body cells as zinc oxide and Silver NPs, which showed a toxic effect on the male reproductive system. Phyllanthus niruri (PN) is a worldwide distributed tropical plant that has multiple pharmacological activities such as anti-malarial and immunomodulator. Previous research obtained significant efficacy by encapsulating PN extract and HBsAg by chitosan NP as co adjuvant to enhance the immune response to hepatitis vaccine. Many studies showed that PN has a toxic effect on the male reproductive system, especially on the Sertoli cell of testis and sperm parameters, and that affects male fertility. There are no studies related to the toxicity of chitosan NP loaded with PN extract on male fertility. The current study was designed to evaluate the toxic effects of chitosan NP loaded with PN extract on sperm characteristics of adult Swiss Webster male mice. This study focused on the preparation and characterization of chitosan NPs loaded with PN extract and in vivo study the nanotoxicological effect on sperm quality. 24 Swiss Webster male mice were divided randomly into six groups of 4 mice and administered treatment intraperitoneally (IP) once daily for 14 days. Group I (control) did not receive treatment, group II received blank nanoparticles 100mg/kg body weight (BW), groups III and IV received PN Extract 25mg/kg BW and 100mg/kg BW respectively, and groups V and VI received PN NP 25mg/kg BW and 100mg/kg BW respectively. The animals were sacrificed, and epididymal sperms were collected and analyzed for sperm count, motility, and morphology. The findings showed that the prepared NPs have a good characteristic as NP size around 178 nm, Polydispersity index (PI) 0.23, Zeta potential +37 mv, and good entrapment efficiency (EE%) 74%. Significant reduction (p < 0.05) in epididymal sperm count and motility in treated groups IV, V, and VI were observed, and significant (p < 0.05) increased in abnormal sperm morphology characterized by no head, no hook, and bent tail were also observed in these treated groups compared to control while no significant (p < 0.05) alteration in sperm quality in groups II and III. Blank chitosan NPs even in high dose, did not show any toxicity on sperm parameters, proving that chitosan NPs are safe on the male reproductive system. In contrast, A high dose of PN extract showed a toxic effect on sperm quality and when loading PN extract in chitosan NPs, even in low dose showed toxicity by altering male fertility parameters, thus altering the reproductive functioning of the sperm cells conferring antifertility properties on the mice.