Janus magnetic nanoparticles (similar to 20 nm) were prepared by grafting either polystyrene sodium sulfonate (PSSNa) or polydimethylamino ethylmethacrylate (PDMAEMA) to the exposed surfaces of negatively charged poly(acrylic acid) (PAA)-coated magnetite nanoparticles adsorbed onto positively charged silica beads. Individually dispersed Janus nanoparticles were obtained by repulsion from the beads on reversal of the silica surface charge when the solution pH was increased. Controlled aggregation of the Janus nanoparticles was observed at low pH values, with the formation of stable clusters of approximately 2-4 times the initial size of the particles. Cluster formation was reversed, and individually dispersed nanoparticles recovered, by restoring the pH to high values. At intermediate pH values, PSSNa Janus nanoparticles showed moderate clustering, while PDMAEMA Janus nanoparticles aggregated uncontrollably due to dipolar interactions. The size of the stable clusters could be controlled by increasing the molecular weight of the grafted polymer, or by decreasing the magnetic nanoparticle surface availability for grafting, both of which yielded larger cluster sizes. The addition of small amounts of PAA-coated magnetic nanoparticles to the Janus nanoparticle suspension resulted in a further increase in the final cluster size. Monte Carlo simulation results compared favorably with experimental observations and showed the formation of small, elongated clusters similar in structure to those observed in cryo-TEM images.