Capillary liquid chromatography with electrochemical detection (CLC-ECD) was developed for determining the femtogram levels of baicalin and baicalein. The CLC-ECD system and the experimental conditions were optimized based on the precision (=information content) phi and efficiency (=information content/time) theta, which were calculated from a relative standard deviation (R.S.D.) by a chemometric tool called the FUMI theory. When CLC-ECD was established using a capillary column (Inertsil ODS-3, 150 mm x 0.2 mm i.d.), a sample injector fitted with a 0.2 microL injection loop, an applied potential of +650 mV vs. Ag/AgCl, and a flow rate at 1.8 microL/min, baicalin and baicalein were determined at femtogram levels. Moreover, the present method was validated using a chemometric tool and a conventional method. Since the FUMI theory makes it possible to predict R.S.D. without repetitive measurements, the chemometric tool saves considerable amounts of chemicals and experimental time, and was found to be useful for the optimization of conditions and validation for determination by CLC-ECD. The present method was applied to the analysis of Japanese Pharmacopoeia Scutellaria Root and Scutellaria baicalensis Georgi for determining baicalin and baicalein.