Magnetic nanosensors have become attractive instruments for the diagnosis and treatment of different diseases. They represent an efficient carrier system in drug delivery or in transporting contrast agents. For such purposes, magnetic nanosensors are used in vivo (intracorporeal application). To remove specific compounds from blood, magnetic nanosensors act as elimination system, which represents an extracorporeal approach. This review discusses principles, advantages and risks on recent advances in the field of magnetic nanosensors. First, synthesis methods for magnetic nanosensors and possibilities for enhancement of biocompatibility with different coating materials are addressed. Then, attention is devoted to clinical applications, in which nanosensors are or may be used as carrier- and elimination systems in the near future. Finally, risk considerations and possible effects of nanomaterials are discussed when working towards clinical applications with magnetic nanosensors.