© 2017 Elsevier B.V.Plant secondary metabolites are an almost unlimited reservoir of potential bioactive compounds. In view of the wide chemical space covered by natural compounds, their comprehensive analysis requires multiple and complementary approaches. In this study, numerous chromatographic conditions were tested for the analysis of a set of 120 representative natural compounds covering a wide polarity range (18 log P units). The experiments were performed on 59 different conditions involving 29 RPLC and HILIC dedicated stationary phases, as well as more exotic mixed mode columns. The best RPLC and HILIC conditions were determined using Derringer's desirability functions, based on various criteria (i.e. retention, peak shape, distribution of compounds during the gradient…). After this first selection, only the most promising conditions were kept (19 in RPLC and 11 in HILIC). The selectivity complementarity among each chromatographic mode was assessed by principal component analysis (PCA) and hierarchical cluster analysis (HCA). In RPLC, a pentabromobenzyl (PBrBz) stationary phase was identified as particularly versatile and could constitute an elegant first intention screening column. Two additional conditions allowed to extend the range of natural compounds space that can be analyzed, while offering better selectivity for basic analytes (hybrid silica graft with C8 moiety operated at pH 9 (Hyb C8)) and acidic compounds (positively charged hybrid silica graft with pentafluorophenyl moiety (Hyb+ PFPh). Although less generic in terms of amenable compounds, an ion exchange/RP mixed mode stationary phase (MM TriP1) offered notably enhanced retention of more polar analytes under RPLC conditions. With these four conditions, 89% of the natural substances were detected by LC–MS with acceptable retentions and peak shapes. In HILIC, four acceptable and complementary conditions were also highlighted. Both Syncro-Z (zwitterionic HILIC phase) and Diol columns were found to offer balanced retention and selectivity for most of the polar compounds (log DpH3 < 1.0). These two columns could be advantageously complemented by hybrid Amide column operated at pH 3 and Amino stationary phase at pH 5, to further enhance both retention and selectivity of polar basic and acidic species, respectively.