Here, we report a generic synthetic approach to rationally design multiply connected and hierarchically branched nanopores inside anodic aluminum oxide templates. By using these nanochannels, we controllably fabricate a large variety of branched nanostructures, far more complex than what exists today. These nanostructures include carbon nanotubes and metallic nanowires having several hierarchical levels of multiple branching. The number and frequency of branching, dimensions, and the overall architecture are controlled precisely through pore design and templated assembly. The technique provides a powerful approach to produce nanostructures of greater morphological complexity, which could have far-reaching implications in the design of future nanoscale systems.