The goal of this study was to compare the performance of three separation techniques for the analysis of 57 hydrophilic compounds. RPLC, hydrophilic interaction liquid chromatography (HILIC) and subcritical fluid chromatography (SFC) were tested. The comparison was based on the retention, selectivity, peak shape (asymmetry and peak width) and MS sensitivity. As expected, RPLC had some obvious limitations for such classes of compounds, and on average the %ACN required to elute these hydrophilic substances was 4, 7, and 11% ACN at pH 3, 6, and 9, respectively. However, a hybrid polar-embedded C18 phase with an appropriate mobile phase could represent a viable strategy for hydrophilic basic compounds with log D greater than -2 on average. HILIC and SFC were found to be more appropriate for analyzing a large majority of these hydrophilic analytes (~60 and 70% of compounds eluted during the gradient in HILIC and SFC), while maintaining good MS sensitivity. Finally, this work demonstrated the complementarity of the three analytical techniques and showed that the selection of a suitable strategy should mostly be based on physicochemical properties of the analytes (pKa, log D, H-bonding capability, etc.).