The unripe fruit of the plant Momordica charantia L., commonly known as bitter gourd or bitter melon, is a popular vegetable and medical herb in many parts of the world and is characterized by its strong bitter taste. In our endeavor to decode its bitter taste, the dichloromethane fraction of 75% methanol extract of bitter gourd was found to be intensely bitter. Combining sensory analysis-guided fractionation and newly developed comparative high-pressure liquid chromatography (HPLC) analysis-guided purification led to the isolation of five known compounds including momordicoside L (1), (23E)-3β-O-malonyl-7β,25-dihydroxycucurbita-5,23-dien-19-al (2), 3-O-β-d-allopyranosyl-7β,25-dihydroxycucurbita-5,23(E)-dien-19-al (3), momordicine IV (5), and charantoside B (6) and three new compounds 3-O-β-d-3-ketoglucopyranosly-7β,25-dihydroxycucurbita-5,23(E)-dien-19-al (4), 6'-O-malonylmomordicoside L (7), and 6'-O-malonylmomordicine IV (8) from bitter gourd. Sensory analysis revealed compounds 3-8 had strong bitter taste with their bitter taste recognition thresholds in the range between 3.6 (4) and 13.6 ppm (6) in 3% ethanol. UPLC-MS/MS quantification showed that their concentration in bitter gourd ranged from 16.5 ± 1.3 mg/kg (4) to 214.8 ± 14.0 mg/kg (6) on a dry weight basis. Calculation of the dose-over-threshold (DoT) factor showed that momordicine IV (5) and charantoside B (6) should be considered as bitter principles of bitter gourd. In addition, the study also demonstrated the ubiquity of the isomerization reaction in the side chain of cucurbitane-type triterpenoids. Many isolated compounds were the isomerized products of their natural precursors, and these precursors should be the primary bitterness contributors of fresh fruits. In addition, comparative HPLC analysis-guided purification could be a practical approach for the fast isolation of acid-labile precursors.