Hierarchical block copolymer self-assembly is used to produce "polyplex-in-hydrophobic-core" (PIHC) micelles for gene delivery. The unique PIHC micelle structure provides nuclease protection and controlled release by embedding nucleic acids in the micelle core surrounded by condensed hydrophobic polymer chains. PIHC micelles are generated through a simple, two-step process using commercially available polymers: (1) electrostatic binding between the nucleic acid cargo and poly(ε-caprolactone)block-poly(2-vinyl pyridine) (PCL-b-P2VP) (SA1), followed by (2) microprecipitation of the polyplex with poly(ε-caprolactone)block-poly(ethylene glycol) (SA2). The resulting vectors possess poly(ethylene glycol) (PEG) coronae and nucleic acid−P2VP polyplexes embedded within condensed PCL hydrophobic cores. Using a two-phase microfluidic reactor for the SA2 step, we produce mainly spherical PIHC micelles with ∼30 nm PCL cores and ∼15 nm PEG shells. Plasmids encapsulated in PIHC micelles show resistance to DNase I degradation compared to plasmids located outside the micelle cores. PIHC micelles containing pUC18 show enhanced transformation efficiencies in competent Escherichia coli with a linear time dependence over 8 h associated with slow plasmid release via hydrolytic degradation of PCL cores. Finally, we show that PIHC micelles are readily taken into the cytosol of MDA-MB-231 (human breast cancer) cells.