Extensive biomedical applications of nanoparticles are mainly determined by their safety and compatibility in biological systems. The aim of this study was to compare the biosafety and biocompatibility of gold nanoparticles (GNPs) prepared with HEPES buffer, which is popular for cell culture, and sodium citrate, a frequent reducing agent. From experimental results on the body weight and organ coefficients of acute oral toxicity tests, it could be observed that HEPES-prepared GNPs are biologically safer than citric-prepared GNPs at the same dose of 500 mu g/kg. The in vitro cell viability was higher for HEPES-prepared GNPs than citric-prepared GNPs at 5.0-and 10.0-ug/mL concentrations. More reactive oxygen species (ROS) were generated in the cell suspension when supplemented with citric-prepared GNPs than HEPES-prepared GNPs when their concentrations were higher than 20 mu g/mL. The results stated that HEPES-prepared GNPs had better biosafety and biocompatibility than citric-prepared GNPs. This study not only revealed the influence of reducing agent on biosafety and biocompatibility of nanomaterials but also provided accumulative evidence for nanomaterials in biomedical applications.