For the first time polyphosphate (poly P) granules have been detected in Helicobacter pylori organisms colonizing the gastric antrum as well as in organisms isolated from the same tissue. Poly P granules showed typical sublimation characteristics during exposure to the electron beam and chipped out of ultrathin sectioning. A prominent phosphorus signal was identified using elemental specific electron microscopy such as electron energy loss spectroscopy (EELS) and was localized to at least three different locations: the cytoplasm, the flagellar pole and in association with the cell membrane. Intracytoplasmatic structures had a diameter of 0.05-0.2 micron, whereas the structures near the flagellar pole were much smaller (0.02 micron). The membrane-associated phosphate aggregates were visible only after staining with Pb(NO3)2 or with electron spectroscopic imaging (ESI). Poly P granules seem to be important energy and phosphorus stores and it is thought that they participate in the regulation of various and distinct metabolic processes of H. pylori.