A new method is presented for the synthesis of monodisperse, size-tunable Fe3O4 spherical nanocluster particles through a simple, one-step hydrothermal reaction, according to a kinetics-controlled self-assembly process of smaller nanocrystals into hierarchical mesoporous aggregates. The mean diameter of the particles can be controlled over a broad range up to ~230 nm by simply varying the concentration of the precipitating reagent (urea or ammonia). The particles can be easily dispersed in water with excellent colloidal stability, exhibit a high surface area of ~ 60 m2 g(-1), and demonstrate size-dependent magnetic separation kinetics, where the larger nanoclusters exhibit rapid magnetophoresis, and the smaller nanoclusters remain inseparable. Thus particle size control is essential for improving magnetic separation processes.