A current goal of relativistic heavy ion collisions experiments is the search for a Color Glass Condensate as the limiting state of QCD matter at very high density. In viscous hydrodynamics simulations, a standard Glauber initial condition leads to estimate $4pi eta/s sim 1$, while a Color Glass Condensate modeling leads to at least a factor of 2 larger $eta/s$. Within a kinetic theory approach based on a relativistic Boltzmann-like transport simulation, we point out that the out-of-equilibrium initial distribution proper of a Color Glass Condensate reduces the efficiency in building-up the elliptic flow. Our main result at RHIC energy is that the available data on $v_2$ are in agreement with a $4pi eta/s sim 1$ also for Color Glass Condensate initial conditions, opening the possibility to describe self-consistently also higher order flow, otherwise significantly underestimated, and to pursue further the search for signatures of the Color Glass Condensate.