Over the last decade, exosomes from diverse biological sources have been proposed as new natural platforms in drug delivery. Translation of these nanometric tools to clinical practice requires deep knowledge of their pharmacokinetic properties and biodistribution. The pharmacokinetic properties of exosomes are sometimes evaluated using biochemical and histological techniques that are considerably invasive. As an alternative, we present radiochemical labeling of milk-derived exosomes based on reduced 99mTc (IV) without modifying biological and physicochemical properties. This approach enables longitudinal tracking of natural exosomes by non-invasive single photon emission computed tomography (SPECT) imaging and the evaluation of their pharmacokinetic properties according to the route of administration.