The conditions to efficiently and reproducibly extract geniposide and genipin in Gardenia fruit powders were established usingTaguchi experimental design approaches to improve extraction recovery. Geniposide, the major iridoid glycoside component of Gardeniafruits, which has been recognized to have choleretic effects, is transformed to Genipin in animals. In this study, the extraction conditionsof geniposide and genipin such as solvent types, solvent acidities and boiling times were investigated under the guidance of experimentaldesigns to obtain the highest content in extracts determined with liquid chromatography-mass spectrometry (LC-MS) methods. Herbalpowders ground from Gardenia fruits, Gardenia jasminoides Ellis and Gardenia jasminoides Ellis var. grandiflora Nakai, were used.This paper has successfully demonstrated the use of Taguchi orthogonal arrays to obtain proper extraction conditions of geniposideand genipin in the above fruits. These design methods are capable of obtaining the optimum extraction conditions in only nine trialsin which three factors, namely solvent type, boiling time and solvent acidity are investigated. The results show that solvent acidity isthe influencing factor in achieving adequate contents and the other factors only have minor influences. The highest content obtained issimilar to the reported data. In addition, using Taguchi orthogonal arrays within four experimental trials has identified that the extractionof ground fine powders results in more reproducible recovery than that of coarse ones.