Abstract The ionic radii of rare earth elements (REE: Sc, Y, and the lanthanides) are key to interpreting partitioning behavior between minerals and melts for use as petrogenetic tracers and thermometry. Of REE, Y commonly has the highest concentration and serves as a reference against which other REE concentrations or partition coefficients can be compared. Here, we show that published experimental data on mineral-melt partitioning of REE imply the ionic radius of Y3+ is smaller than commonly assumed by 0.001 Å for sixfold coordination to 0.005 Å for eightfold and ninefold coordination. This difference reconciles the partitioning behavior of Y3+ with that of other REE and improves reference states for interpreting trace element systematics in rocks. Thermobarometry can be highly sensitive to assumed ionic radii, and downward correction of the Y3+ ionic radius improves some REE-based temperatures by hundreds of degrees. Future studies that employ the most common tabulations of ionic radii of the REE (Shannon 1976) should use an ionic radius of Y3+ of 0.899, 1.014, and 1.070 Å for six-, eight-, and ninefold coordination, respectively; alternatively, the ionic radius of Y can be scaled to that of Ho3+ × 0.9984. More generally, trace element partitioning data, coupled with theoretical models, provide an exact method for refining effective relative ionic radii in minerals where direct structural determinations are not possible.