Resource recovery and wastewater purification of agricultural waste are currently considered important ways to reduce environmental impact. In the present study, hydrogen fermentation of cow manure mixed with various defined substrates or artificial food wastes was examined by lab-scale batch mode experiments at 60°C, using hydrogen-producing bacteria naturally present in the manure. A variety of carbohydrates including cellulose and xylan were used as substrates for hydrogen production, although no hydrogen production was observed with proteinous substrates (casein, gelatin and albumin), an amino-acid mixture (Casamino acids), or lipids (palmitic acid, linoleic acid, soybean oil, and olive oil). In experiments involving artificial food wastes (boiled rice, bread, cabbage, chicken meat, fish meat, egg, mayonnaise, chocolate, and strawberry jam), the amounts of hydrogen production were positively correlated with the carbohydrate content of the foods, while no significant correlation with protein or fat content was observed. To examine the effect of hydrogen fermentation on methane fermentation, a two-step treatment (hydrogen fermentation followed by methane fermentation) was conducted using cow manure mixed with dog food. The hydrogen fermentation increased methane production two-fold as compared with the one-step treatment (methane fermentation only). In addition, the hydrogen fermentation enhanced the removal of volatile solids and biochemical oxygen demand from the mixture, suggesting that hydrogen fermentation has advantages in wastewater purification.