We have performed time-domain interferometry experiments with matter waves trapped in an harmonic potential above and below the Bose-Einstein phase transition. We interrogate the atoms according to the method of separated oscillating fields, with a sequence of two radio-frequency pulses, separated by a time delay T . We observe the oscillation of the population between two internal Zeeman states, as a function of the delay T .We find a strong depletion of the interference fringes for both the Bose condensates and the thermal clouds above condensation, even at very short times, when the clouds are still overlapping. Actually, we explain the observed loss of contrast in terms of phase patterns imprinted by the relative motion, as a consequence of the entanglement between the internal and external states of the trapped atoms. 03.75.Fi, 05.30.Jp, 32.80.Pj, 34.20.Cf The question about the coherence of Bose-Einstein condensates (BECs) [1], and the characterization of their phase properties have drawn considerable attention in the recent literature.The first evidence of a definite phase for weakly interacting condensates dates back to the experiment of the MIT group [2], where high contrast matter-wave interference fringes were observed in the density distribution of two freely expanding BEC's. Subsequent experiments performed at JILA [3,4] measured the relative phase of two condensate in different internal (hyperfine) states experiencing almost the same trapping potential.Other experiments have further investigated this subject [5,6,7,8]. In particular, the group of W. Phillips has recently measured the evolution of the spatial profile of the phase of BEC's, by using a Bragg-interferometer [7]. They have shown that a trapped condensate is characterized by a uniform phase, and after release from the trap develops a non-uniform phase profile.In a recent Letter [9] we have demonstrated an experimental method for a sensitive and precise investigation of the interaction between two Bose-Einstein condensates [10]. In this paper we present an interferometry experiment performed in the time-domain on the same system, which allows to gain a deeper insight into Ramsey interferometry [11] with ultra-cold atoms across the BEC phase transition.It is well known that Ramsey fringes are readily observable with a sample at room temperature. The reason is that Ramsey signals rely on the persistence of coherence between two distinct atomic levels, no matter what the state of the particles center-of-mass is. This is true only when the internal and external degrees of freedom are uncoupled. Whenever the latter condition fails, a depletion of the Ramsey fringes visibility can occur and has indeed been observed [12]. Thus, the entanglement of external and internal states of atoms trapped in a magnetic potential is the basis for the use of Ramsey method to characterize the phase properties of a condensate and a thermal cloud near BEC. In the JILA experiment [3], such an entanglement caused the observed Ramsey fringes in the population of ...