Magnetic resonance imaging (MRI) has become a powerful technique in biological molecular imaging and clinical diagnosis. With the rapid progress in nanoscale science and technology, nanostructure-based MR contrast agents are undergoing rapid development. This is in part due to the tuneable magnetic and cellular uptake properties, large surface area for conjugation and favourable biodistribution. In this review, we describe our recent progress in the development of high-performance nanostructured MR contrast agents. Specifically, we report on Gd-enriched nanostructured probes that exhibit T1 MR contrast and superparamagnetic Fe3O4 and CoFe2O4 nanostructures that display T2 MR contrast enhancement. The effects of nanostructure size, shape, assembly and surface modification on relaxivity are described. The potential of these contrast agents for in vitro and in vivo MR imaging with respect to colloidal stability under physiological conditions, biocompatibility, and surface functionality are also evaluated.