A systematic study with laser ablation—ICP-MS, scanning electron microscopy and electron microprobe revealed that ∼70–95 wt% of REE (except Eu), Y, Th and U in granite rocks and crustal protoliths reside within REEYThU-rich accessories whose nature, composition and associations change with the rock aluminosity. The accessory assemblage of peraluminous granites, migmatites and high-grade rocks is composed of monazite, xenotime (in low-Ca varieties), apatite, zircon, Thorthosilicate, uraninite and betafite-pyrochlore. Metaluminous granites have allanite, sphene, apatite, zircon, monazite and Thorthosilicaie. Peralkaline granites have aeschinite, fergusonite, samarskite, bastnaesite, fluocerite, allanite, sphene, zircon, monazite, xenotime and Th-orthosilicate. Granulite-grade garnets are enriched in Nd and Sm by no less than one order of magnitude with respect to amphibolite-grade garnets. Granulitegrade feldspars are also enriched in LREE with respect to amphibolite-grade feldspars. Accessories cause non-Henrian behaviour of REE, Y, Th and U during melt—solid partitioning. Because elevated fractions of monazite, xenotime and zircon in common migmatites are included within major minerals, their behaviour during anatexis is controlled by that of their host. Settling curves calculated for a convecting magma show that accessories are too small to settle appreciably, being separated from the melt as inclusions within larger minerals. Biotite has the greatest tendency to include accessories, thereby indirectly controlling the geochemistry of REE, Y, Th and U. We conclude that REE, Y, Th and U are unsuitable for petrogenetical modelling of granitoids through equilibrium-based trace-element fractionation equations.