There is a need for a rapid, accurate and reliable method for quantitative lipid fingerprinting in the light of current interest in microalgae-based biofuels. It is important to characterize the lipids in algal biomass as a measure to assess its suitability as biofuel feedstock. We are developing fast, high-throughput methods for extraction and profiling of microalgal lipids, using accelerated solvent extractions, rapid derivatization methods and ultra-fast GC. Traditional fatty acid analyses require large amounts of biomass, are slow and not tailored towards the comprehensive lipid analysis needed in algal biofuels research. A high-throughput analytical platform is required to identify candidate algal species with the appropriate lipid composition from a growing collection of largely uncharacterized strains and secondly assess the effect on the lipid profile of a large matrix of environmental variables. We are presenting results showing an automated extraction method optimized for highest lipid yield using different solvents. We are in the process of optimizing an efficient derivatization method for the analysis of fatty acid methyl esters (FAMEs) by gas chromatography. We are presenting results from a comparison between direct biomass derivatization and lipid based derivatization methods with regards to yield and fatty acid profile obtained.