This is a protocol for quantitating total lipids in microalgae. The acid-dichromate method is widely used to perform colorimetric analysis of extracted lipids. Here we present a protocol using 96-well microtiter plate for safe and efficient sample handling with high throughput. Only 500 ul of 0.15% acid-dichromate is required for each sample, which greatly reduces the amount of corrosive and toxic reagent. In addition, comparing with the absorbance at 440 nm, the absorbance at 348 nm yields five-time higher sensitivity in lipids quantitation.Total lipids in the samples should not excess 80 ug. Accurate quantitation can be achieved with as little as 20 ug. A working detection limit is about 5 ug.