The authors describe a multiphase density gradient centrifugation method for the separation and purification of hybrid nanoparticles (NPs). The method was applied to the purification of NPs consisting of magnetite gold NPs of type Fe 3 O 4 @Au and coated with 1-dodecylthiol. A density gradient has been established by forming cushions of a multicomponent solution composed of (a) a nonlinear gradient of sucrose in the of 5-50 % concentration range, (b) a constant concentration of ficoll (a neutral, highly branched, high-mass, hydrophilic polysaccharide; 30 % w/w), and (c) a constant concentration of percoll (colloidal silica particles coated with polyvinylpyrrolidone; 15 % w/w). The final separation profiles are adjusted via dynamic differential centrifugation at 4480×g for 30 min. The mixture of NPs to be separated is added and centrifuged at 2520×g for 40 min. This will separate the NPs into five fractions together with other secondary components. The fractions were characterized by FTIR, XPS, and SEM-EDX techniques. Finally, a continuous flow system with resonance light scattering detection was established and coupled to the separation system in order to monitor the separated fractions.