This overview covers the different chemometric strategies linked to chromatographic methodologies that have been used and presented in the recent literature to cope with problems related to incomplete separation, the presence of unexpected components in the sample, matrix effect and changes in the analytical signal due to pre-treatment of sample.Among the different chemometric strategies it focuses on pre-treatment of data to correct background and time shift of chromatographic peaks and the use of second-order algorithms to cope with overlapping peaks from analytes or from analytes and interferences in liquid chromatography coupled to diode array, fast-scanning fluorescence spectroscopy and mass spectrometry detectors.Finally the review presents the strategies used to deal with changes in the analytical response as result of matrix effect in liquid and gas chromatography, as well as the use of standardization strategies to correct modifications in the analytical signal as a consequence of sample pre-treatment in liquid chromatography.