We show that contrary to first expectations realistic three generation supersymmetric intersecting brane world models give rise to phenomenologically interesting predictions about gauge coupling unification. Assuming the most economical way of realizing the matter content of the MSSM via intersecting branes we obtain a model independent relation among the three gauge coupling constants at the string scale. In order to correctly reproduce the experimentally known values of sin^2[theta_W(M_z)] and alpha_s(M_z) this relation leads to natural gauge coupling unification at a string scale close to the standard GUT scale 2 x 10^16 GeV. Additional vector-like matter can push the unification scale up to the Planck scale.