Conventional optical microscopy at visible wavelengths suffers from severe resolution limitations in that features on scales smaller than about 200 nm cannot be resolved. Since cell receptor proteins, amyloid structures, and other important cellular actors are much smaller, there has been a need for higher resolution. The relatively new method of “super-resolution” fluorescence microscopy has circumvented this resolution limit allowing visualization of detail down to the 20-40 nm range. Super-resolution microscopy can be achieved by stimulated emission depletion, structured illumination, or single-molecule localization microscopy methods. These approaches can now be used to explore structures that could not be observed previously, in both normal and diseased cells. Specific applications to bacterial protein superstructures, huntingtin aggregates, and other cellular targets will be described, along with potential applications to cancer-related structures.