In order to use the photosynthetic cyanobacterium Synechocystis as a source of feedstock for carbon-neutral, nonpetroleum-based diesel fuel, we evaluated several solvents and solvent systems for their ability to extract lipid from wild-type Synechocystis PCC 6803. Chloroform + methanol-based Folch and Bligh & Dyer methods had the highest lipid recoveries. Less toxic solvents, such as methanol and MTBE, or direct trans-esterification of biomass (without pre-extraction step) gave only slightly lower lipid-extraction yields. Ethanol, isopropanol, butanol, hexane, acetic ester, and their combinations were not effective for lipid extraction from Synechocystis (>20% loss), even though they are widely used for non-polar lipid extraction from other feedstock, including algae. We confirmed the success of chloroform + methanol-based extraction by their penetration of the cell membrane system, higher polarity, and stronger interaction with hydrogen bonds. The less-polar solvents not only had lower lipid yield, but also extracted more non-lipid compounds that require extra purification to remove. We also characterized the fatty-acid profile of Synechocystis PCC 6803: C16:0 (similar to 60%), C16:1 (similar to 9.5%), C18:0 (similar to 1.2%), C18:1 (similar to 2%), C18:2 (similar to 9.8%), and 08:3 (similar to 16.5%). (C) 2010 Elsevier Ltd. All rights reserved.