In this talk I will first review the regularisation procedure that allows one to formulate the initial value problem for higher derivative theories of gravity, including theories with higher-than-second order equations of motion, in a way such that it is well-posed. I will then explain how this method can be extended to scalar-tensor theories of gravity and I will show how to apply it to the most general scalar-tensor theory of gravity up to four derivatives of the fields, including parity-violating terms. This theory includes Einstein-scalar-Gauss-Bonet gravity and Dynamical Chern-Simons theories, both of which have received some attention in the community. In the final part of my talk, I will show some preliminary results of black hole binary mergers in these theories.