Since the discovery of perchlorate in water system, the public has been concerned about its human health effect. In practice it was reported that chronic exposure to perchlorate may lead to damage in thyroid hormone activity. This study introduced a method of perchlorate reduction, using autotrophic bacteria which utilise hydrogen as an electron donor. Two experiments were conducted to compare the effects of acute and chronic perchlorate toxicity on bacterial perchlorate reduction potential. One was a batch-fed operation generating acute toxicity and another was a continuous-fed operation generating chronic toxicity. Acclimation period of the batch-fed operation was 14 days while that of the continuous-fed operation was 31 days as commensurate with double. Lots of batch tests using the mixed culture passing through acclimation were conducted to figure out kinetics of biological perchlorate reduction. The maximum perchlorate utilisation rate (q(max)) of the mixed culture acclimated by acute toxicity was 2.92 mg ClO(4)/mg dry-weight (DW)/d, while that of chronic toxicity was 0.27 mg ClO(4)/mg DW/d. Half-maximum rate constants (K(s)) of acute and chronic toxicity were 567.3 and 25.6 mg ClO(4)(-)/L respectively. This result showed that acute toxicity acclimated the mixed culture more rapidly and produced a higher activity for biological perchlorate reduction than chronic toxicity.