Cross-linked potato starch nanocapsules with encapsulated dsDNA (with a defined number of base pairs, i.e., 286, 476, and 790 bp) were synthesized using the miniemulsion technique. The inverse (water-in-oil) miniemulsion system was applied to create stable aqueous nanodroplets of dissolved starch in cyclohexane as a continuous phase. The amphiphilic block copolymer poly[(ethylene-co-butylene)-b-(ethylene oxide)] was used as a surfactant to stabilize the droplets. After addition of the cross-linker, 2,4-toluene diisocyanate (TDI), the polyaddition reaction took place at the droplet's interface, resulting in the formation of a polymeric cross-linked shell. The influence of starch, surfactant, and the amount of cross-linker on the average size, size distribution, and morphology of the capsules was studied by dynamic light scattering and electron microscopy. FTIR spectroscopy was used to identify the chemical composition of the capsule shell. The permeability of the shell was studied on the fluorescent dye (i.e., sulforhodamine 101) containing capsules using fluorescence spectroscopy. High thermal stability of the cross-linked capsules allows one to perform the polymerase chain reaction inside the core. The encapsulation of dsDNA and the efficiency of the PCR were confirmed by fluorescence spectroscopy after staining with the DNA-selective dye (SYBRGreen).