The advent of 2.5-D and 3-D integration has allowed for the development of complex heterogeneous systems, where intellectual property (IP) across multiple vendors and from different process nodes and foundries are placed side-by-side. Although such integration opens the door to enhanced circuit functionality, concerns in the physical security of such systems, which was already of concern with 2-D integrated circuits, becomes of greater significance. The potential for sourcing and integrating adversarial IP including hardware Trojans, placing untrusted ICs, leaking critical circuit functionality or user data through side-channels, or even allowing for attack through exploitation of side-channels must be considered. In this paper, a thorough analysis of the security vulnerabilities of 2.5-D and 3-D integrated systems is provided, with the goal of the highlighting the importance of considering the security implications of such systems during design.