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Economically productive alternatives to gin trash and manure disposal would benefit both the ginning and dairy industries. Combining gin and dairy wastes in a two-phase anaerobic system produces methane gas and a class A soil amendment. Gin and dairy wastes were combined in a parameter optimization experiment to quantify potential methane gas production and process time. The process reached completion in three weeks when temperatures were above 32 C (90 F), mixture ratios below 5:1 (gin to dairy waste, dry basis) and the solid phase was wetted twice daily. Ten percent of the mass was converted to soluble chemical oxygen demand (COD), which has potential for conversion to methane in the second phase. Larger scale trials resulted in 48% of the combined waste being converted into methane, or 87 m3 CH4 per ton of combined waste. Under mesophilic conditions the average methane concentration in the produced gas was 72% (due to excluding the respiration gases of the acidifiers from the methane production reactor). Combining manure with cotton gin waste results in 35% higher gas production per unit of digester volume. A third set of experiments confirmed accelerated pathogen reduction due to the presence of gin trash. Seeding pasteurized combinations of manure and gin trash and manure and cellulose with E. coli O157:H7 in small scale single phase laboratory reactors demonstrated the disinfecting property of gin trash. After 12 days E. coli O157:H7 was undetectable in the reactors containing gin trash and manure. The reactors containing cellulose and manure took 20 days to reach O157:H7 levels that were below detection levels by both selective media and polymerase chain reaction amplification.