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Background: Selenium nanoparticles (Se NPs) and selenium nanocomposites (Se NCs) have different biological effects. The current study aimed to compare the effects of newly synthesized Se NPs and Se NCs on biochemical and histopathological parameters of rats. The synthesized Se NPs were characterized by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), energy dispersive X-ray analysis (EDAX), and scanning electron microscopy (SEM) techniques. Materials and Methods: Adult male Wistar rats were divided into four equal groups to examine the biological effects of Se NPs. Control rats received saline intraperitoneally while experimental rats were received four-week intraperitoneal injections of Se powder, Se NPs, and Se NCs at the dose of (0.4 mg/kg). After four weeks, serum was obtained by the conventional methods, and then rats were sacrificed to separate liver, kidney, and testis tissues for histopathological examinations. Results: The intraperitoneal injection of Se powder caused significant elevations in serum liver enzyme levels, serum blood urea nitrogen (BUN) lipid peroxidation, and serum creatinine levels (P<0.05). The histopathological investigations showed necrosis and fatty change in liver. Kidney sections showed cytoplasmic vacuolation and hyaline casts, and the testis sections showed degeneration of seminiferous tubules. Se NPs intraperitoneal injections at a dose of 0.4 mg/kg caused no significant effects on liver enzymes, malondialdehyde (MDA) content, and histopathological changes while significantly increased serum BUN and creatinine levels (P<0.05). The group treated with Se NCs showed normal biochemical and histopathological parameters (P<0.05). Conclusion: The current study proved the toxicity of Se powder; however, nano-formulations of Se showed fewer side effects.