A procedure to stain oyster larvae Crassostrea virginica with the fluorescent, lipid-specific dye Nile Red was developed. Experiments were performed to select for optimal carrier solvent, staining time, stain concentration, fixation regime and time of observation under the fluorescence microscope. The technique allows relative quantification of lipids in individual larvae. The optimal staining technique was: Nile Red dissolved in acetone applied on live larvae (unfixed and starved for 6 h prior to staining), at a concentration of 1.25 mug/ml, staining for 1.5 h, and fluorescence measurements within 4 h after staining. Up to 1000 larvae can be analysed per day.