The composition of anaerobic granules and their EPS was investigated when the granules were exposed to long term depletion of selected heavy metals (Ni, Co and Fe) in upflow anaerobic sludge blanket (UASB) reactors. Experiments were performed in five reactors (R1-R5). Granules in reactors were operated at the following conditions: (1) fed with volatile fatty acids supplemented with yeast extract for over 200 days, (2) the same feed, but without yeast extract, for 60 days and (3) no feeding but upflow liquid recirculation for 30 days. Feed for each reactor was supplemented with different concentrations of Ni, Co and Fe. Supplements of Ni, Co and Fe in the feed did not influence the COD conversion in the reactors for 200 days. However, when yeast extract was eliminated from the feed, COD conversion decreased significantly after 60 days in these reactors which were not supplemented with iron. Amount of carbohydrates extracted from granules was affected by iron and yeast extract. A good relationship was found between the extracted carbohydrates and specific activity of bacteria. Most of the iron and cobalt in extracted EPS were found in bound form, which may be important in bacterial aggregation. The polysaccharides in EPS contained mainly pentoses and hexoses.