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Low concentrations of the long-chain fatty acids oleate and stearate inhibited all steps of the anaerobic thermophilic biogas process during digestion of cattle manure. The lag phase increased when the concentrations of oleate and stearate were 0.2 g/l and 0.5 g/l, respectively, and no growth was found at concentrations of 0.5 g/l for oleate and 1.0 g/l for stearate. The toxic effect of these acids was permanent as growth did not occur when inhibited cultures were diluted to a non-inhibitory concentration. No adaptation to the fatty acids toxicity was observed by pre-exposing the cultures to non-inhibitory concentrations and the inhibitory response was the same as for cultures not pre-exposed to the fatty acids. Oleate was less inhibitory when added as a neutral oil in the form of the glycerol ester. This indicates that it is the free fatty acid that influences the bacterial activity.