The aim of this thesis is to develop an approach for computing correlation functions of quantum integrable lattice models within the quantum version of the Separation of Variables (SoV) method. SoV is a powerful method which applies to a wide range of quantum integrable models with various boundary conditions. Yet, the problem of computing correlation functions within this framework is still widely open. Here, we more precisely consider two simple models solvable by SoV: the XXX and XXZ Heisenberg chains of spins 1/2, with anti-periodic boundary conditions, or more generally quasi-periodic boundary conditions with a non-diagonal twist. We first review their solution by SoV, which present some similarities but also crucial differences. Then ...