A rapid, simple and sensitive spectrofluorimetric technique was developed for monitoring total lipids in hyphae of the riboflavin-overproducing fungus Eremothecium ashbyii using the fluorescent probe Nile blue in an aqueous system, avoiding the interference due to autofluorescent riboflavin. The existing methodologies for lipid estimation are tedious, requiring large biomass, solvent extraction and gravimetry. E. ashbyii is a hemiascomycete fungus which accumulates lipids in its mycelia prior to flavinogenesis. This study defines the conditions (wavelength selection and sensitivity) for the spectrofluorimetric quantification of lipids in situ in the macerated mycelia of this fungus in the presence of intracellular autofluorescent riboflavin without the need to extract the lipids from the mycelia. The fluorescent intensity was linear with the lipid concentration of the mycelia (by gravimetry) under three different growth conditions using glucose, olive oil and sunflower oil as carbon sources. This spectrofluorimetic method of lipid estimation can be applied to other fungi and microorganisms. © 2003 Elsevier Science B.V. All rights reserved.