Although there are a number of reports regarding the toxicity evaluation of inorganic nanoparticles, knowledge on biodegradable nanomaterials, which have always been considered safe, is still limited. For example, the toxicity of chitosan nanoparticles, one of the most widely used drug/gene delivery vehicles, is largely unknown. In this report, we examined the cytotoxic effects of chitosan nanoparticles on mouse embryos at the blastocyst stage and in vivo implantation by embryo transfer. Blastocysts treated with 250 nm chitosan nanoparticles exhibited significantly increased apoptosis and a corresponding decrease in total cell number, which was concentration‐dependent. Moreover, the TUNEL positive signal in the embryos exposed to chitosan nanoparticles showed an increased of the ICM and the implantation success rate was lower than that of their control counterparts. Our results collectively indicate that in vitro exposure to chitosan nanoparticles induces apoptosis and retards implantation development after transfer to host mice. The results collectively show that chitosan nanoparticles have the potential to induce embryo cytotoxicity. Further studies are required to establish effective protection strategies against the cytotoxic effects of these nanoparticles.