Plant secondary metabolites are an almost unlimited reservoir of potential bioactive compounds. In viewof the wide chemical space covered by natural compounds, their comprehensive analysis requires mul-tiple and complementary approaches. In this study, numerous chromatographic conditions were testedfor the analysis of a set of 120 representative natural compounds covering a wide polarity range (18log P units). The experiments were performed on 59 different conditions involving 29 RPLC and HILICdedicated stationary phases, as well as more exotic mixed mode columns. The best RPLC and HILIC con-ditions 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 mostpromising conditions were kept (19 in RPLC and 11 in HILIC). The selectivity complementarity amongeach chromatographic mode was assessed by principal component analysis (PCA) and hierarchical clusteranalysis (HCA). In RPLC, a pentabromobenzyl (PBrBz) stationary phase was identified as particularly ver-satile and could constitute an elegant first intention screening column. Two additional conditions allowedto extend the range of natural compounds space that can be analyzed, while offering better selectivityfor 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 genericin terms of amenable compounds, an ion exchange/RP mixed mode stationary phase (MM TriP1) offerednotably 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. InHILIC, four acceptable and complementary conditions were also highlighted. Both Syncro-Z (zwitterionicHILIC phase) and Diol columns were found to offer balanced retention and selectivity for most of thepolar compounds (log DpH3< 1.0). These two columns could be advantageously complemented by hybridAmide column operated at pH 3 and Amino stationary phase at pH 5, to further enhance both retentionand selectivity of polar basic and acidic species, respectively.