In LC method development, the choice of suitable experimental onditions is often challenging for the analyst because of the huge diversity of stationary phases, mobile phase pH and organic modifiers, that could significantly alter the selectivity. The influence of these parameters on selectivity was experimentally tested in both RPLC and HILIC conditions for the analysis of 45 pharmaceutical compounds covering a wide range of physico-chemical properties. Principal component analysis (PCA) models were built to assess the resulting multivariate dataset. The complementarity between RPLC and HILIC was clearly demonstrated. The importance of mobile phase pH as one of the main experimental factors to be considered was confirmed. The RPLC and HILIC methods were thus employed for the analysis of a drug cocktail containing two substrates and their numerous desmethylated metabolites. All the compounds were finally resolved in both modes, with a very distinct elution order. In addition, the possibility to combine columns of different selectivity was highlighted using a column coupler set-up and found to be extremely promising. The same type of experiments was also carried out for the impurity profiling of an antihistaminic drug. In this example, compounds of very distinct polarity were satisfactorily eluted in both RPLC and HILIC modes, using suitable conditions of pH and stationary phase. In conclusion, this study demonstrates the complementary and interest of RPLC and HILIC in the case of pharmaceutical method development.