A fast and simple method for white wine differentiation based on fingerprinting by means of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) combined with linear time-of-flight (TOF) mass spectrometry (MS) and statistical interpretation of the obtained data using principal component as well as cluster analysis is presented. A systematic development was performed to allow a direct comparison and classification of 33 Croatian white wines based on MALDI linear TOF mass spectra (“assuming protein/peptide fingerprints”) in the positive ion mode. α-Cyano-4-hydroxycinnamic acid as a MALDI matrix in solution mixed with the unmodified (without any dilution or preconcentration or purification/isolation) white wine sample in a volume ratio 1:1 was applied at ambient conditions and this volume sample preparation technique provided the highest mass spectral information content and optimal reproducibility. Several MALDI matrices, solvents and preparation techniques were evaluated with the selection of the above mentioned as the optimum, prior to large scale investigations. Data obtained by statistical analysis of the aligned mass spectrometric data are shown to provide an efficient way to differentiate white wines of Croatian origin.