Methods and systems for realizing a high brightness, compact x-ray source suitable for high throughput, in-line x-ray metrology are presented herein. A compact electron beam accelerator is coupled to a compact undulator to produce a high brightness, compact x-ray source capable of generating x-ray radiation with wavelengths of approximately one Angstrom or less with a flux of at least 1e10 photons/s*mm^2. In some embodiments, the electron path length through the electron beam accelerator is less than ten meters and the electron path length through the undulator is also less than 10 meters. The compact x-ray source is tunable, allowing for adjustments of both wavelength and flux of the generated x-ray radiation. The x-ray radiation generated by the compact x-ray source is delivered to the specimen over a small spot, thus enabling measurements of modern semiconductor structures.