This study evaluates the effect of aeration pretreatment to prepare an inoculum for H-2 and CH4 production in a two-stage process. Moreover, the biochemical hydrogen potential and biochemical methane potential of waste from the food industry in a two-stage process was assessed. The results confirmed the possibility of using an aerobic stress for selecting a hydrogen-producing inoculum. The inoculum was fairly stable since no hydrogenotrophic-methanogenic activity was observed in 25 days. The yields measured using glucose as substrate were of approximately 160 and 280NmL(H2)g(COD)(-1) of glucose for hydrogen and methane, respectively, which are in agreement with other studies using heat-shock for the pretreatment of the inoculum. When waste of the food industry (wheat milling) was used as substrate, a lower H-2 yield was achieved by the aerobically-pretreated inoculum if compared to heat-shock; however, when combined with methane production in a two-stage process, much higher CH4 yield was achieved. (C) 2014 Elsevier Ltd. All rights reserved.