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In this paper, the problem of acquiring the pilot and data channel of the next-generation systems (as Galileo, and GPS modernization) is addressed and analyzed, focusing the majority of the attention to the problem of managing the higher sign reversal transition rate due to the navigation message in the data channel and to the secondary code in the pilot channel. It must be considered that in the case of the Galileo E1 signals, each period of the spreading sequence may suffer of a sign change which can reduce the correlation gain. Moreover, the sign transition occurred on the block of samples being processed produces a correlation peak splitting along the Doppler axis of the search space matrix constructed during the acquisition phase and this may lead to a wrong Doppler estimate. Here, we propose an acquisition detection methodology in order to cope with the aforementioned impairments. The main idea behind the proposed algorithm derives by the fact that even though a sign transition occurs, the total useful signal energy remains unchanged, so it is possible to process the search space in order to recover in a nonambiguous way not only the presence of a satellite but also the correct spreading code delay phase and its Doppler shift. The effectiveness of the proposed method will be deeply assessed with a simulation campaign in terms of detection and false detection rate, which will be presented by means of the so-called receiver operative characteristic curves and compared with the state-of-the-art acquisition methodologies.