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Despite the numerous advantages of employing nanomaterials in pharmaceutical sciences, some studies have revealed the possible toxicity of nanomaterials. There is a gap between the spectacular qualities of nanotechnology and nanotoxicity, which should be bridged in order to assure the safety of nanomaterials in human health. Phyllanthus niruri is a medicinal plant that has traditionally been used as an anti-malarial, dissolving kidney stones and immunomodulator. The present work was determined to investigate potential cytotoxicity and genotoxicity of Phyllanthus niruri extract loaded nanoparticles (PNNP) and Phyllanthus niruri extract nanoemulsions (PNNE) on mouse Sertoli cell line (TM4) and their potential adverse impact on spermatogenesis. The study concept is to formulate and characterize chitosan nanoparticles loaded with Phyllanthus niruri extract, as well as Phyllanthus niruri nanoemulsions of two sizes. The cytotoxicity on Sertoli cells was determined using a colorimetric technique, Cell Counting Kit-8. The cell viability of blank (empty) nanoemulsions and blank nanoparticles was determined by trypan blue exclusion dye staining. Fast halo and comet assays were used to quantify single-strand DNA breaks (SSBs) in Sertoli cells to determine potential genotoxicity of Phyllanthus niruri nanomaterials (nanoparticles and nanoemulsions). To detect changes in cell morphology during apoptosis, Hoechst 33342 staining was performed. An immunofluorescence assay was used to examine the expression of blood-testis barrier (BTB) proteins (connexin 43, claudin 11) in TM4 cells after exposure to PNNP 125 ppm and PNNE with diameters of 163.7 nm and 16.9 nm at a concentration of 125 ppm. According to the findings, the synthesized PNNP has good characteristics such as a NP size of 170.6 nm, a polydispersity index (PI) of 0.269, a Zeta potential of +37.8 mv, and a good entrapment efficiency (EE) of 71.0%. PNNE was successfully formulated with two diameters of 163.7 nm and 16.9 nm, a polydispersity index (PI) of 0.291 and 0.181, a zeta potential of -9.1 mv and -5.7 mv, and a high entrapment efficiency (EE %) of 89% and 93%. The results showed that PNNP and PNNE exposure induce DNA damage in Sertoli cell line (TM4), as determined by Fast halo and Comet assays, as well as apoptosis, as determined by changes in cell morphology as confirmed by Hoechst 33342 staining. There was significant down regulation of BTB proteins in Sertoli cells after exposure to PNNP, PNNE at concentration of 125 ppm which could compromise the integrity of BTB and subsequently disrupt spermatogenesis process in male.