The enantiomers of catechin and epicatechin were separated by chiral capillary electrophoresis using modified cyclodextrins as chiral selectors. Various conditions for the separation system were optimized, including the pH value and the concentration of the running buffer. A baseline separation of the catechin and epicatechin enantiomers could be achieved by using 0.1 mol l−1 borate buffer (pH 8.5) with 12 mmol l−1 (2-hydroxypropyl)-γ-cyclodextrin as chiral selector, a fused-silica capillary with 40 cm effective length (75 μm I.D.), +18 kV applied voltage, a temperature of 20 °C and direct UV detection at 280 nm. The method was applied to different plant food samples. (+)-Catechin and (−)-epicatechin could be verified as the most common flavan-3-ols. In the case of guaraná, however, we were able to identify all four enantiomers, both (+)- and (−)-catechin and (+)- and (−)-epicatechin, as naturally occurring compounds. This finding was verified by further isolation and purification of the flavan-3-ols and subsequent LC–MS analysis. This method allows for the identification of the authenticity of guaraná through the analysis of the catechin and epicatechin enantiomers, additionally to the conventional methods like HPLC.