Nanomaterials have been widely used in the biomedical field as gene/drug carriers, magnetic resonance imaging (MRI) contrast reagents, photothermal therapy reagents, fluorescent cellular markers, etc. The origins and working mechanisms of cytotoxicities of nanomaterials, however, are not well understood. It is often stated in the literature that a nanomaterial is non-toxic and biocompatible. In this study, we show that the short term cytotoxicity of a nanomaterial is determined by the surface functionality, rather than the core nanomaterial. A so-called "non-toxic and biocompatible" nanomaterial, such as core/shell iron-filled carbon nanoparticles (Fe@CNPs) and nanodiamonds (NDs), can become cytotoxic when a cationic surface functionality, such as imidazolium (IM) and tertiary methyl ammonium ethyl methacrylate (TMAEA) moieties, was grafted onto the surface. To investigate the contributions of surface functionalities and the core nanomaterials on cytotoxicity, two "non-toxic and biocompatible" Fe@CNPs and NDs were surface-modified with different surface functionalities, including anionic COOH, zwitterionic PVP, neutral OH, cationic IM and TMAEA, and investigated for their cytotoxicities in both in vitro cancer cells (HeLa and U-87MG cells) and in vivo embryo development of zebrafish. Among these surface functionalities, cationic IM and TMAEA functionalities of both Fe@CNPs and NDs cause acute cytotoxicity to a similar extent in the in vitro cancer cell experiments, as well as affect severely the embryonic development and survival rates of zebrafish. Other surface functionalities do not show particularly strong cytotoxicities. To obtain information regarding the origins of cytotoxicities, the effects of surface functionalities were also examined on the lactate dehydrogenase (LDH) levels, cellular ROS generation, apoptosis, and changes in lysosomal membrane integrity, mitochondrial membrane potential, the intracellular pH (pH i), and cell cycles. Our results clearly point out that surface functionality, rather than the core nanomaterials, plays a critical role in dictating the short-term cytotoxicities. © 2014 The Royal Society of Chemistry.