The orchid genus Brachystele Schltr. comprises 20 species distributed from Mexico to Argentina; 10 are found in Brazil. Anatomical studies of Orchidoideae Lindl. have been scarce, and the anatomy and histochemistry of Brachystele are still largely unknown. We characterized the vegetative organs of B. guayanensis (Lindl.) Schltr. using standard anatomical and histochemical microtechniques. Brachystele guayanensis was observed to display the anatomical characters commonly found in the vegetative organs of representatives of the Orchidaceae and Orchidoideae (including a uniseriate epidermis, thin cuticle, amphistomatic leaves, anomocytic, diacytic and tetracytic stomata, a homogeneous mesophyll, collateral vascular bundles, rhizomes with pericyclic fibers, roots with velamen, uniseriate exodermis, endodermis and pericycle). Histochemical tests confirmed the presence of lignin, proteins, and alkaloids, the lipidic nature of the cuticle, starch grains stored in spiranthosomes in the roots, and the composition of the raphides. Alkaloids were observed in great abundance, especially in the roots, and may have potentially useful medicinal activities, as has been observed in groups phylogenetically related to Brachystele.