Even though on many farms increasing the temperature of vast quantities of cold influent streams to thermophilic (55°C) levels may not be feasible, thermophilic anaerobic digestion has been important for energy recovery from Danish agricultural wastes (Ahring et al. 1992; Angelidaki and Ahring 1992, 1993, 1994; Hansen et al. 1999; Ahring et al. 2001t. The advantage of thermophilic anaerobic digestion lies in the superior kinetic rates at higher temperatures because of improved hydrolysis rates and methane yields (Vandevoorde and Verstraete 1987; Mackie and Bryant 1995; Sung and Santha 2003). Therefore, thermophilic digesters have been found to improve solids destruction over mesophilic digesters (35-37°C; Angelidaki and Ahring 1994; Sung and Santha 2003 t. Thermophilic digestion of animal wastes would also allow for sufficient pathogen destruction and the generation of biosolids that can easily be dispersed into the environment (Han and Dague 1997; Welper et al. 1997). However, protein-rich wastewater treatment at thermophilic conditions has shown to be problematic. Because of digestion of proteins into the end-product ammonia, higher levels of free ammonia at thermophilic compared with mesophilic temperatures (with similar total ammonia concentrations) have inhibited methanogenesis and caused unstable performances (Zeeman et al. 1985; Angelidaki and Ahring 1993; Lettinga 1995; Zitomer et al. 2005; Bocher et al. 2008). Acetate oxidation at thermophilic conditions may alleviate these unstable conditions somewhat because thermophilic hydrogenotrophic methanogens can tolerate higher levels of ammonia than mesophilic hydrogenotrophic methanogens (Hendriksen and Ahring 1991) and we already know that in general the hydrogenotrophic methanogens can tolerate ammonia better than acetoclastic methanogens (Sprott and Patel 1986). Despite possible acetate oxidation, ammonia inhibition at thermophilic conditions remains a real problem. In Denmark, mixing carbon-rich waste streams with protein-rich animal wastes to “dilute” the concentrations of the fermentation end-product ammonia has solved this problem. A report by Lindorfer et al. (2008) investigated the increase in operating temperature beyond mesophilic temperatures by self-heating anaerobic digesters fed with energy crops. They found that short temperature pulses and addition of acclimated biomass can circumvent negative effects of high free ammonia concentrations to digester performance during periods of increasing temperatures.