To characterize lipid content of microalgal cells rapidly and accurately, the gravimetric determination, FT-IR and Nile Red (NR) staining were investigated on six typical eukaryotic and prokaryotic algae species. FT-IR and Nile Red were relative quantification methods and a standard curve was required in contrast to the gravimetric method. The FT-IR method determined the lipid, carbohydrate and protein contents simultaneously assuming that the algal cells only consisted of those three components. The Nile Red method was a relatively rapid method for neutral lipid content characterization by spectrofluorometry and could locate lipid body of the algal cell by fluorescence microscopy. According to sample sources and processing purposes, the gravimetric determination was preferable for large-scale cultivation with low-frequency monitoring, while FT-IR and Nile Red were suitable for general laboratory cultivation with medium-frequency monitoring, in particularly Nile Red was appropriate for small samples when high-frequency screening was required. (C) 2012 Elsevier Ltd. All rights reserved.