Gold nanomaterials (Au NMs) have attracted increasing attention in biomedicine due to their facile preparation, multifunctional modifications, unique optical and electrical properties, and good biocompatibility. The physicochemical properties of Au NMs at nanoscale, like size, shape, surface chemistry, and near field effects, are rendering Au NMs potent candidates in biomedicine. Thus, risk assessment of negative effects of Au NMs on biological systems is becoming urgent and necessary for future applications. In this review, we summarize up-to-date progresses on the preparation and modification of Au NMs and their biomedical applications, including biosensor, bioimaging and phototherapy, gene/drug delivery. Finally, we discuss the potential risk of Au NMs to biological systems, which is instructive for rationally designing and preparing nanomaterials for safe applications in nanomedicine.