We study the stationary scattering theory for the matrix Schrodinger equation on the half line, with the most general boundary condition at the origin, and with integrable selfadjoint matrix potentials. We prove the limiting absorption principle, we construct the generalized Fourier maps, and we prove that they are partially isometric with initial space, the subspace of absolute continuity of the matrix Schrodinger operator, and final space L-2 ((0,infinity)). We prove the existence and the completeness of the wave operators and we establish that they are given by the stationary formulae. We also construct the spectral shift function and we give its high-energy asymptotics. Furthermore, assuming that the potential also has a finite first moment, we prove a Levinson's theorem for the spectral shift function. (C) 2015 AIP Publishing LLC.