We ask the question of how the (weak) equivalence principle established in classical gravitational physics should be reformulated and interpreted for massive quantum objects that may also have internal degrees of freedom (dof). This inquiry is necessary because even elementary concepts like a classical trajectory are not well defined in quantum physics-trajectories originating from quantum histories become viable entities only under stringent decoherence conditions. From this investigation we posit two logically and operationally distinct statements of the equivalence principle for quantum systems. Version A: the probability distribution of position for a free-falling particle is the same as the probability distribution of a free particle, modulo a mass-independent shift of its mean. Version B: any two particles with the same velocity wave-function behave identically in free fall, irrespective of their masses. Both statements apply to all quantum states, including those without a classical correspondence, and also for composite particles with quantum internal dof. We also investigate the consequences of the interaction between internal and external dof induced by free fall. For a class of initial states, we find dephasing occurs for the translational dof, namely, the suppression of the off-diagonal terms of the density matrix, in the position basis. We also find a gravitational phase shift in the reduced density matrix of the internal dof that does not depend on the particle s mass. For classical states, the phase shift has a natural classical interpretation in terms of gravitational red-shift and special relativistic time-dilation.