We investigated the effect of organic anions as spray liquid additives on the ionization efficiency of unconjugated, glycine-conjugated and taurine-conjugated bile acids under electrospray ionization conditions. Addition of organic acids influenced the ionization efficiency of whole bile acids. Use of a stronger acid reduced the peak intensity of unconjugated and glycine-conjugated bile acids, while the use of TFA, the strongest acid tested, improved the intensity of taurine conjugates. The hydroxyl group at the C-12 alpha position of cholic acid and deoxycholic acid easily underwent intra-molecular hydrogen bonding with the side chain carboxyl group, accelerating the ionization efficiency. This intra-molecular hydrogen bond may also affect the formation of product ions in low energy-CID. The addition of ammonium ions to the spray liquid influenced the ionization of all bile acids, specifically enhancing the ionization efficiency of unconjugated bile acids.