Nanostructured hydrogels have been developed as synthetic tissues and scaffolds for cell and drug delivery, and as guides for tissue regeneration. A fundamental problem in the development of synthetic hydrogels is that implanted gel structure is difficult to monitor noninvasively. This work demonstrates that the aggregation of magnetic nanoparticles, attached to specific macromolecules in biological and synthetic hydrogels, can be controlled to detect changes in gel macromolecular structure with MRI. It is further shown that the gels can be made to self‐degrade when they come into contact with a target molecule in as low as pM concentrations. The sensitivity of the gels to the target is finely controlled using an embedded zymogen cascade amplifier. These “MRI reporter gels” may serve as smart, responsive polymer implants, as tissue scaffolds to deliver drugs, or to detect specific pathogens in vivo. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.