Interest in applications for the simultaneous acquisition of data from different devices is growing. In neuroscience for example, co-registration complements and overcomes some of the shortcomings of individual methods. However, precise synchronization of the different data streams involved is required before joint data analysis. Our article presents and evaluates a synchronization method which maximizes the alignment of information across time. Synchronization through common triggers is widely used in all existing methods, because it is very simple and effective. However, this solution has been found to fail in certain practical situations, namely for the spurious detection of triggers and/or when the timestamps of triggers sampled by each acquisition device are not jointly distributed linearly for the entire duration of an experiment. We propose two additional mechanisms, the "Longest Common Subsequence" algorithm and a piecewise linear regression, in order to overcome the limitations of the classical method of synchronizing common triggers. The proposed synchronization method was evaluated using both real and artificial data. Co-registrations of electroencephalographic signals (EEG) and eye movements were used for real data. We compared the effectiveness of our method to another open source method implemented using EYE-EEG toolbox.