We report the cross-linking of hydrophobic compartments of complex self-assembled structures of amphiphilic block copolymers (BCPs) by the [2 pi + 2 pi]-cycloaddition of indene moieties present in a hydrophobic block based on polystyrene (PS). A photodimerizable indene group was introduced to the PS block by controlled radical copolymerization of indanolylstyrene, which was subsequently dehydrated to indenylstyrene using the Burgess reagent. This mild conversion producing the photodimerizable indene pendant groups ensured the synthesis of BCPs with a photo-cross-linkable PS block. We demonstrate that the micellar structures and complex inverse bicontinuous bilayers of BCPs containing hydrophobic PS cores could be covalently cross-linked in aqueous solutions upon irradiation with long-wavelength UV light (lambda = 365 nm). The procedure formed an infinite polymer network within the hydrophobic compartments of the self-assembled nanostructures without using any additional reagents or causing morphological changes during the cross-linking. A wide variety of self-assembled structures retained their structural integrity in common organic solvents after cross-linking of the hydrophobic PS blocks.