In the present study, direct flow injection mass spectrometry was investigated for rapid characterization of the polyphenolic composition of red wines. Atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI) (in both positive and negative ion modes) have been simultaneously used for a more comprehensive analysis of the samples studied. In this way, four mass spectra have been recorded for each wine. Each spectrum was considered as a fingerprint related to the chemical composition. This methodology was applied to a large number of Beaujolais wines from different grades and different vintages. This data set was processed using a chemometrical multiblock analysis, which allowed to synthesize the whole information collected. The results obtained showed that the wine fingerprints address the composition of the main polyphenolic compounds present in the red wines and can discriminate groups of wines showing different polyphenolic compositions. Multiblock analysis appears as a very promising tool to deal with several data tables of multivariate signals in order to define, by combining the whole information, the best operating protocol according to the desired analytical objectives.