A two-stage process to produce hydrogen and methane from lipid-extracted microalgal biomass residues (LMBRs) was developed. The biogas production and energy efficiency were compared between one- and two-stage processes. The two-stage process generated 46 +/- 2.4 mL H(2)/g-volatile solid (VS), and 393.6 +/- 19.5 mL CH(4)/g-VS. The methane yield was 22% higher than the one in the one-stage process. Energy efficiency increased from 51% in the one-stage process to 65% in the two-stage process. Additionally, it was found that repeated batch cultivation was a useful method to cultivate the cultures to improve the methane production rate and reduce the fermentation time. In the repeated batch cultivation, the methane yield slightly decreased if the ammonia levels rose, suggesting that the accumulation of ammonia could affect methane production. Crown Copyright (C) 2010, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.