Although there has been a large research effort associated with individual parts of various algal biofuel production pathways, few studies have tracked changes in product composition throughout an integrated biofuel production process. This study uses microscopy and chromatography to analyze the progression of lipid profile and cell structure of algal cells throughout a research-scale production pathway for biocrude. For the specific processing methods used in this pathway, it is shown that TAG content decreased, while DAG and FFA content increased during processing. The changes in the lipid content corresponded to cell degradation that was observed by SEM and TEM throughout processing. These results demonstrate the dynamic nature of lipid composition in an algal culture used for biofuel production and emphasize the need to monitor changes in lipid profile, as those changes can directly impact biofuel productivity. (C) 2012 Elsevier Ltd. All rights reserved.