Lipids from microalgae are a suitable feedstock for biofuel production. Some algal strains can produce up to 60% of their weight in lipids under favorable growth conditions, a trait that could be desirable for fuel production. In order to accelerate the screening process of high lipid containing microalgae a procedure combining Percoll density gradient and Nile red spectrofluorometry was evaluated. Native Chlorella sp. was grown under nitrogen-replete (2.94mM) and nitrogen deplete (1 mM) conditions. Cells were separated by buoyant density on a Percoll step gradient (100, 80, 60 and 10% v/v) and lipid content of the bands was estimated by measuring emitted fluorescence using Nile red spectrofluorometry. Cultures with increased lipid production (nitrogen depletion) generated lipid peaks (∼570nm) and reached equilibrium at 10% Percoll whereas cells with low lipid content (nitrogen sufficiency) emitted no fluorescence and layered at 80% Percoll. The difference in banding pattern indicates that cell buoyant density is due to lipid content. This method is a practical tool for rapid screening of high lipid containing microalgae.