The dispersion of magnetic nanoparticles (NPs) in homopolymer poly(methyl methacrylate) (PMMA) and block copolymer poly(styrene-b-methyl methacrylate) (PS-b-PMMA) films is investigated by TEM and AFM. The magnetite (Fe3O4) NPs are grafted with PMMA brushes with molecular weights from M = 2.7 to 35.7 kg/mol. Whereas a uniform dispersion of NPs with the longest brush is obtained in a PMMA matrix (P = 37 and 77 kg/mol), NPs with shorter brushes are found to aggregate. This behavior is attributed to wet and dry brush theory, respectively. Upon mixing NPs with the shortest brush in PS-b-PMMA, as-cast and annealed films show a uniform dispersion at 1 wt%. However, at 10 wt%, PS-b-PMMA remains disordered upon annealing and the NPs aggregate into 22 nm domains, which is greater than the domain size of the PMMA lamellae, 18 nm. For the longest brush length, the NPs aggregate into domains that are much larger than the lamellae and are encapsulated by PS-b-PMMA which form an onion-ring morphology. Using a multi-component Flory–Huggins theory, the concentrations at which the NPs are expected to phase separate in solution are calculated and found to be in good agreement with experimental observations of aggregation.