New hardware security threats are identified in emerging threedimensional (3D) integrated circuits (ICs) and potential countermeasures are introduced. Trigger and payload mechanisms for future 3D hardware Trojans are predicted. Furthermore, a novel, network-on-chip based 3D obfuscation method is proposed to block the direct communication between two commercial dies in a 3D structure, thus thwarting reverse engineering attacks on the vertical dimension. Simulation results demonstrate that the proposed method effectively obfuscates the cross-plane communication by increasing the reverse engineering time by approximately 5× as compared to using direct through silicon via (TSV) connections. The proposed method consumes approximately one fifth the area and power of a typical network-on-chip designed in a 65 nm technology, exhibiting limited overhead.