Natural enrichments of magnetotactic bacteria were used to study the sites where heavy metals accumulate in uncultured bacteria. Most bacteria obtained by magnetic concentration from these enrichments contained, in addition to the magnetosomes, large phosphorus-rich granules in the cytoplasm. Metal (Zn, Mn, Sr, Cd, Al, Cr, and Pb) chlorides were added independently to the enrichments, and after 24 h, the elemental composition of the phosphorus-rich granules, magnetosomes, and "soft parts" (cytoplasm plus cell envelope) of whole bacteria was analyzed by energy-dispersive X-ray analysis on a transmission electron microscope. All bacteria contained Mn and Sr in the phosphorus-rich granules; some of them presented Mn peaks also in the soft parts. Zinc accumulation was variable and was found mainly in the phosphorus-rich granules, but also in the soft part of some bacteria. Some analyzed bacteria presented Zn peaks only in the soft parts, and some of them did not present Zn in any structure. Cadmium and Al were found only in the granules of some bacteria. Chromium was found in the soft parts of some bacteria. Lead was not detected in any bacteria. We concluded that the phosphorus-rich granules are major sites for metal accumulation by these bacteria. No conclusive results for magnetosomes were obtained because of the limitations of the analytical techniques particularly when used for whole cell analysis.