This work is an exploration of how graphs and permutations can be applied in the context of quantum information processing. In Chapter 2 we consider problems about the permutations of the subsystems of a quantum system. Explicitly, we attempt to understand the problem of determining if two quantum states of N qubits are isomorphic: if one can be obtained from the other by permuting its subsystems. We show that the well known graph isomorphism problem is a special case of state isomorphism. We also show that the complement of state isomorphism, the problem of determining if two states are not isomorphic, can be verified by a quantum interactive proof system, and that this proof system can be made statistical zero knowledge. We also consider the complexity of isomorphism problems for stabilizer states, and mixed states. In Chapter 3 we work with a special class of quantum states called grid states, in an effort to develop a toy model for mixed state entanglement. The key idea with grid states is that they can be represented by what we call a grid-labelled graph, literally, a graph forced to have vertices on a two dimensional grid. We show that whether or not a grid state is entangled can sometimes be determined solely from the structural properties of its corresponding grid-labelled graph. We use the grid state framework to build families of bound entangled states, suggesting that even in this restricted setting detecting entanglement is non-trivial and will require more than a single entanglement criterion.