This paper focuses on the practical aspects and implications of preprocessing chromatographic data to correct for undesirable time-shifts. An approach to automate the alignment of chromatographic data based on peak alignment or warping is proposed. This approach deals with selection of the required parameters including selection of reference sample to warp towards, and chooses warping settings based on a new evaluation criterion for goodness of correction. The new criterion aims at quantifying goodness of alignment while at the same time penalising significant shape or area-changes in the warped peaks. The entire selection procedure is automated using a discrete-coordinates simplex-like optimisation routine. Examples with simulated chromatographic data, GC-FID and HPLC-Fluorescence measurement series illustrate the potential of using this automated alignment tool. (C) Copyright 2007 John Wiley & Sons, Ltd.