An x-ray transmission spectrometer system to be used with a compact x-ray source to measure x-ray absorption with both high spatial and high spectral resolution. The spectrometer system comprises a compact high brightness x-ray source, an optical system with a low pass spectral filter property to focus the x-rays through an object to be examined, and a spectrometer comprising a crystal analyzer (and, in some embodiments, a mosaic crystal) to disperse the transmitted beam, and in some instances an array detector. The high brightness/high flux x-ray source may have a take-off angle between 0 and 15 degrees, and be coupled to an optical system that collects and focuses the high flux x-rays to micron-scale spots, leading to high flux density. The x-ray optical system may also act as a “low-pass” filter, allowing a predetermined bandwidth of x-rays to be observed at one time while excluding the higher harmonics.