The accurate characterization of nanolayered systems is an essential topic for today’s developments in many fields of material research. Thin high-k layers and gate stacks are technologically required for the design of current and future electronic devices and can be deposited, e.g., by Atomic Layer Deposition (ALD). However, the metrological challenges to characterize such systems demand further development of analytical techniques. Reference-free Grazing Incidence X-ray Fluorescence (GIXRF) based on synchrotron radiation can significantly contribute to the characterization of such nanolayered systems. GIXRF takes advantage of the incident angle dependence of XRF, in particular below the substrate’s critical angle where changes in the X-ray Standing Wave field (XSW) intensity influence the angular intensity profile. The reliable modeling of the XSW in conjunction with the radiometrically calibrated instrumentation at the PTB allows for reference-free, fundamental parameter-based quantitative analysis. This approach is very well suited for the characterization of nanoscaled materials, especially when no reference samples with sufficient quality are available. The capabilities of this method are demonstrated by means of two systems for transistor gate stacks, i.e., Al2O3 high-k layers grown on Si or Si/SiO2 and Sc2O3 layers on InGaAs/InP substrates.