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Magnetic Resonance Imaging (MRI) is a powerful, noninvasive and nondestructive technique, capable of providing three-dimensional (3D) images of living organisms. The use of magnetic contrast agents has allowed clinical researchers and analysts to significantly increase the sensitivity and specificity of MRI, since these agents change the intrinsic properties of the tissues within a living organism, increasing the information present in the images. Advances in nanotechnology and materials science, as well as the research of new magnetic effects, have been the driving forces that are propelling forward the use of magnetic nanostructures as promising alternatives to commercial contrast agents used in MRI. This review discusses the principles associated with the use of contrast agents in MRI, as well as the most recent reports focused on nanostructured contrast agents. The potential applications of gadolinium- (Gd) and manganese- (Mn) based nanomaterials and iron oxide nanoparticles in this imaging technique are discussed as well, from their magnetic behavior to the commonly used materials and nanoarchitectures. Additionally, recent efforts to develop new types of contrast agents based on synthetic antiferromagnetic and high aspect ratio nanostructures are also addressed. Furthermore, the application of these materials in theragnosis, either as contrast agents and controlled drug release systems, contrast agents and thermal therapy materials or contrast agents and radiosensitizers, is also presented.