The differentiation of the secretory cavities of Ginkgo stem and the structural organization of the epithelial cells were followed by light and electron microscopy. The mode of formation of the cavities is schizo-lysigeneous. Functional complexes of leucoplasts and associated endoplasmic reticulum (ER) membranes are assumed to be the site of synthesis and translocation of the lipophilic secretory product. Most of the endoplasmic reticulum membranes are paired. The content of the cavities was directly collected and analysed by low- and high-resolution mass spectrometry. The cavities contain anacardic acids and cardanols, which are long-chain phenol lipids not characteristic of Ginkgo. The relationship between the plastid/ER complexes and the production of these secondary metabolites is discussed.