Fuels from microalgae are being considered as important alternatives to fossil fuels. In this work we have identified challenges and opportunities for research in the production of energy from microalgae. The most important challenge facing this alternative resource is the energy generation efficiency (EGE) when microalgae are used for the generation of energy. EGE is about 35% for coal fired power plants while integrated gasification fuel cell cycle (IGFC) and advanced-IGFC (A-IGFC) have an efficiency of over 50%. Other challenges include, achieving a high titer of 2 g/1, a high lipid content of up to 30% and a high CO2 mass transfer efficiency. We observed that the process of energy generation from microalgae has good positive energy balance if the EGE can be improved to greater than 50% by developing IGFC/A-IGFC technologies. Other challenges come from energy spent in dewatering, loss of energy when solvents are recycled during the process of lipid extraction, use of energy in the form of methanol and energy used in recycling excess methanol if biodiesel is produced, and energy used in the production of nutrients, among others. Hence, future research must be targeted at minimizing the energy input in these processes. (C) 2017 Elsevier Ltd. All rights reserved.