Hydrogen can be produced through fermenting sugars in a mixed bacterial culture under anaerobic conditions. Anaerobic granular sludge was proposed as immobilized hydrogen producing bacteria to be used in hydrogen fermentation after methanogenic activity of the granule was eliminated in the pretreatment process. This paper reports an innovative treatment method to directly convert methanogenic granules to hydrogen producing granules using chloroform. Chloroform treatment was compared against acid and heat treatments of sewage sludge and methanogenic granules in terms of effectiveness to eliminate methanogenic activity. The results showed that chloroform treatment was the most effective among the three methods tested. Acid and heat treatments that were effective for sewage sludge treatment were observed not highly effective for application to granules because of the protection from the granular structure. In contrast, methanogens were very sensitive to the chloroform even at very low level. Methane production was almost completely inhibited in both sewage sludge and granules with the treatment with only 0.05% chloroform addition into the culture medium. If the chloroform concentration was controlled at low levels, chloroform selectively inhibited methanogenic activity while did not affect the hydrogen production. At high concentration range, chloroform also inhibited hydrogen production. Chloroform caused irreversible methanogenic activity elimination but hydrogen production recovered to normal after chloroform addition stopped. Chloroform showed desirable selectivity on inhibition of methanogens from hydrogen producing bacteria, nearly permanently eliminated the methane production, postponed the hydrogen consumption to acetic acid, while allowed recovery for normal hydrogen production. Chloroform treated granules were repeatedly cultured for eight time without noticeable damage. Continuous culture with chloroform treated granules showed that the granule structure could be kept for over 15 days and new granules started to form after 10 days operation. The hydrogen productivity reached 11.6L/L/day at HRT 5.3h, which all showed potential application of chloroform treatment of methanogenic granules in the immobilized hydrogen fermentation. (C) 2007 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved.