We present a micro-x-ray fluorescence (XRF) system having a high-brightness x-ray illumination system with high x-ray flux and high flux density. The higher brightness is achieved in part by using x-ray target designs that comprise a number of microstructures of x-ray generating materials fabricated in close thermal contact with a substrate having high thermal conductivity. This allows for bombardment of the targets with higher electron density or higher energy electrons, which leads to greater x-ray flux. The high brightness / high flux x-ray source may then be coupled to an x-ray optical system, which can collect and focus the high flux x-rays to spots that can be as small as one micron, leading to high flux density at the fluorescent sample. Such systems may be useful for a variety of applications, including mineralogy, trace element detection, structure and composition analysis, metrology, as well as forensic science and diagnostic systems.