Ion microprobe U-Pa measurements in zircon crystals from a Holocene rhyolite (Salton Buttes, California) are utilized to assess the partitioning of Pa and U between zircon and melt. The relative sensitivity factor (RSF) for ion microprobe U-Pa zircon analysis was calibrated on a natural high-U secular equilibrium zircon from Buff Peak (Nevada). Zircon crystals from Salton Buttes rhyolite show evidence for excess 231Pa with a weighted average (231Pa)/(235U) activity ratio of 1.9. From this ratio, model zircon-melt partition coefficient ratios DPa/DU = 0.9–2.2 are obtained, assuming plausible limits for (231Pa)/(235U)melt and correcting for the age of zircon crystallization (~15 ka). These values roughly fit lattice strain models for tetravalent cations, but are more than one order of magnitude lower than predictions for pentavalent Pa. Based on this appraisal of Pa partitioning, initial 231Pa disequilibrium caused by zircon-melt fractionation alone can produce minor discordance or excess 207Pb in Late Cenozoic zircon, but is insignificant for older U-Pb zircon ages.