Poly(thioether-ester) (PTEe) nanoparticles obtained by thiol-ene polymerization have received attention of many researchers due to several advantages, including, biocompatibility and biodegradability. The search for new nanomaterials requires toxicity studies to assess potential toxic effects of their administration. Therefore, the aim of this study was to evaluate the in vivo acute toxicity of PTEe and poly(thioetherester)-coated magnetic nanoparticles prepared by thiol-ene polymerization in miniemulsion. These nanoparticles presented a mean size of approximately 120 nm, spherical morphology, and negative surface charge. Doses of 40 mg/kg were administered intraperitoneally to Swiss mice and nociceptive, behavioral and biochemical parameters were investigated in five different organs. None of the nanoparticles led to any alterations in the nociceptive and behavioral responses. Biochemical alterations were observed in liver, decreasing the sulfhydryl and glutathione (GSH) levels, suggesting the dependence of the GSH metabolism in the elimination of the nanoparticles. In general, both nanoparticle types did not cause disturbances in biochemical parameters analyzed in others organs. These results suggest that both nanoparticle types did not induce acute toxicity to the different organs evaluated, reinforcing the biocompatibility of PTEe nanoparticles synthetized by thiol-ene polymerization.