The emerging field of nanomedicine requires better understanding of the interface between nanotechnology and medicine. Better knowledge of the nano-bio interface will lead to better tools for diagnostic imaging and therapy. In this review, recent progress in understanding of how size, shape, and surface properties of nanoparticles (NPs) affect intracellular fate of NPs is discussed. Gold nanostructures are used as a model system in this regard since their physical and chemical properties can be easily manipulated. The NP-uptake is dependent on the physiochemical properties, and once in the cell, most of the NPs are trafficked via an endo-lysosomal path followed by a receptor-mediated endocytosis process at the cell membrane. Within the size range of 2-100 nm, Gold nanoparticles (GNPs) of diameter 50 nm demonstrate the highest uptake. Cellular uptake studies of gold nanorods (GNRs) show that there is a decrease in uptake as the aspect ratio of GNRs increases. Theoretical models support the size- and shape-dependent NP-uptake. The intracellular transport of targeted NPs is faster than untargeted NPs. The surface ligand and charge of NPs play a bigger role in their uptake, transport, and organelle distribution. Exocytosis of NPs is dependent on size and shape as well; however, the trend is different compared to endocytosis. GNPs are now being incorporated into polymer and lipid based NPs to build multifunctional devices. A multifunctional platform based on gold nanostructures, with multimodal imaging, targeting, and therapeutics; hold the possibility of promising directions in medical research.