Transesterification of lipids is a vital step during the processes of both biodiesel production and fatty acid analysis. By comparing the yields and fatty acid profiles obtained from microalgal oil and dry microalgal cells, the reliability of method for the transesterification of micro-scale samples was tested. The minimum amount of microalgal cells needed for accurate analysis was found to be approximately 300 mu g dry cells. This direct transesterification method of fresh cells was applied to eight microalgal species, and the results indicate that the efficiency of the developed method is identical to that of conventional method, except for Spirulina whose lipid content is very low, which means the total lipid content should been considered. (C) 2014 Elsevier Ltd. All rights reserved.