A major challenge in the development of central nervous system drugs is to obtain therapeutic effective drug concentrations inside the brain. Many potentially effective drugs have never reached clinical application because of poor brain penetration. Currently, devices are being developed that may improve drug delivery into the brain. One approach involves the encapsulation of drugs into nanocarriers that are targeted to the brain, where the drug is released. Alternatively, living cells have been engineered to produce the pharmaceutical of interest at the target site. It is important to follow the fate of these drug delivery devices inside the body to verify their efficiency in reaching the brain. To this end, both ex-vivo approaches and in-vivo imaging techniques are used, including ex-vivo biodistribution, autoradiography, MRI, optical imaging, PET and SPECT. All these methods have their specific advantages and limitations. Consequently, selection of the tracking method should be based on the specific aims of the experiment. Here, we will discuss the methods that are currently applied for tracking brain drug delivery devices, including the most commonly used labels and labeling procedures for living cells and nanocarriers. Subsequently, we will discuss specific applications in tracking drug delivery devices.