The quality of a chemical reference material relies on the fact that the composition of the material is homogeneous across all scales. A series of different techniques have been used to evaluate the trace element homogeneity of the GJ-1 reference zircon from the micron- to atomic scale. Cathodoluminescence imaging was conducted along with quantitative crystallographic orientation analysis and trace element analysis using laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS). The nanometre-scale homogeneity was evaluated by analysing five mineral tips using atom probe tomography, which provides atomic scale three dimensional chemical reconstructions with unprecedented spatial resolution. Results show that the GJ-1 reference zircon is homogeneous at all scales, both structurally and chemically. Crystallographic orientation data confirms that this gem quality zircon has no detectable internal crystallographic orientation changes such as crystal-plastic deformation features or cracks. No mineral inclusions were found. Atom probe tomography shows that there is a lack of any chemical clustering or other modes of spatially defined elemental accumulation or depletion for the most abundant trace elements such as Y, Yb and Hf. This finding is supported by LA-ICPMS data revealing homogeneity within the analytical precision. Trace elements of significant abundance include P, Yb, Y, U and Hf, with contents of 30±6, 65±2, 238±5, 284±14 and 6681±57ppm, respectively. Hence, the GJ-1 zircon used as a reference zircon for UPb and Hf-isotopic studies is also a suitable zircon reference material for trace element analyses.