H-2 and ethanol production from glycerol-containing wastes discharged after a manufacturing process for biodiesel fuel (biodiesel wastes) using Enterobacter aerogenes HU-101 was evaluated. The biodiesel wastes should be diluted with a synthetic medium to increase the rate of glycerol utilization and the addition of yeast extract and tryptone to the synthetic medium accelerated the production of H-2 and ethanol. The yields of H-2 and ethanol decreased with an increase in the concentrations of biodiesel wastes and commercially available glycerol (pure glycerol). Furthermore, the rates of H-2 and ethanol production from biodiesel wastes were much lower than those at the same concentration of pure glycerol, partially due to a high salt content in the wastes. In continuous culture with a packed-bed reactor using self-immobilized cells, the maximum rate of H-2 production from pure glycerol was 80 mmol/l/h yielding ethanol at 0.8 mol/mol-glycerol, while that from biodiesel wastes was only 30 mmol/l/h. However, using porous ceramics as a support material to fix cells in the reactor, the maximum H-2 production rate from biodiesel wastes reached 63 mmol/l/h obtaining an ethanol yield of 0.85 mot/mol-glycerol.