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  Poly(N-isopropylacrylamide) (PNIPAM) microgel is perhaps the most well-known intelligent soft nanomaterial. Combining the strengths of hydrogel and nanoparticles, with unique stimuli-responsivity, PNIPAM microgels have found numerous biomedical applications, such as drug delivery, biosensing, and so on. Usually they were used as dispersed particles, however, they can also be used as building blocks to fabricate 2D films and 3D aggregates. These nanostructured assemblies exhibit new properties which the dispersed particles do not have, and new biomedical applications have been found for these assemblies. In this paper, the biomedical applications of PNIPAM microgels in the form of dispersed particles, 2D films and 3D aggregates were reviewed and some recent progress in this area was highlighted.