The functionality, assembly, and fabrication of functional nanoparticles are of increasing interest for a wide range of application areas and there is currently a strong scientific focus on the fundamental properties of such particles. Magnetite (Fe3O4) nanoparticles are especially useful in a wide range of fields, including drug delivery systems, diagnostics, gene analysis, proteomics, separation, purification, hyperthermia therapy, in vivo imaging, and photonics. In many cases it is not the individual nanoparticles themselves that are useful, since they generally do not respond strongly to magnetic fields, but small clusters of these nanoparticles that are more responsive to moderate magnetic fields. We report here the controlled preparation of 100 nm clusters of monodisperse 5 – 10 nm magnetite nanoparticles, in which the morphology can be controlled by selection of the synthesis conditions. Specifically, we have prepared spherical nanoclusters of these nanoparticles with controlled packing characteristics (amorphous or crystalline superlattices), doughnut-shaped nanoclusters, monolayer and multilayer-coated polymer beads, and, finally, Janus nanoparticles with one face consisting of a regular array of nanoparticles, and the other devoid of these nanoparticles. These 100 nm nanoclusters respond to applied magnetic fields to form chains structured in accord with theoretical predictions.