The Ekpyrotic scenario assumes that our visible Universe is a boundary brane in a five-dimensional bulk and that the hot Big Bang occurs when a nearly supersymmetric five-brane travelling along the fifth dimension collides with our visible brane. We show that the generation of isocurvature perturbations is a generic prediction of the Ekpyrotic Universe. This is due to the interactions in the kinetic terms between the brane modulus parametrizing the position of the five-brane in the bulk and the dilaton and volume moduli. We show how to separate explicitly the adiabatic and isorcuvature modes by performing a rotation in field space. Our results indicate that adiabatic and isocurvature pertubations might be cross-correlated and that curvature perturbations might be entirely seeded by isocurvature perturbations.