The National Accelerator Centre (NAC) proton microprobe has been carefully calibrated by the analysis of pure element, primary steel and geological standards. The results obtained are generally accurate to within 5%. For routine analyses (6–8 min), detection limits in the X-ray energy region 7–20 keV, range from 1.5 to 5 ppm. Previous workers have suggested the use of a (H 2) + beam for semi-quantitative analysis and imaging as higher beam brightness is obtainable with this beam at NAC. However, insufficient suppression of electrons introduces significant analytical error. Only a 3 MeV H + beam has been used for the quantitative analysis reported in this work. A rare suite of xenoliths, consisting of interlayered kyanite-bearing and kyanite-free eclogite, from the Roberts Victor kimberlite, Northern Cape, South Africa, was prepared as polished thin-sections and analyzed by the proton microprobe as a pilot study of trace element signatures in its component minerals (garnet, clinopyroxene and kyanite). The analysis of these eclogites identified significant chemical differences between the minerals of the kyanite-bearing and kyanite-free eclogite. Two clear groupings were distinguished well outside statistical error for Mn, Zn and Zr in garnet, and Mn, Ga, Sr and Ba in the clinopyroxene. Furthermore, clear chemical gradients in the elements Mn, Fe, Zn, Y and Zr were identified in single garnets at the contact between the two eclogite types. True elemental imaging revealed a heterogeneous distribution of the elements Sr and Ba in the clinopyroxene; the presence of Ba is interpreted to indicate the introduction of foreign material. A compositional dependence of the partitioning of Zn between garnet and clinopyroxene was also identified. The data do not contradict a previous hypothesis that the kyanite eclogite zones are the metamorphic products of a plagioclase-rich crystal protolith, but they do challenge the proposal that the layering is a primary feature of the rock, diffusion calculations show that these gradients were created in a geologically short time prior to kimberlite emplacement.