A new process is described for the two phase extraction of ergosterol and trehalose from microbial biomass. Baker's yeast was used as a model organism to develop the method, which was then applied for extracting 13 oleaginous microbes. Major findings of the study were that the ergosterol content was not dependent on intracellular oil content and that 1-butanol and alkaline pH were needed to protect ergosterol. Saponification for 3-4. h at 85-100. °C followed by extraction of the reaction mixture with toluene gave the maximal ergosterol yield. Trehalose was stable at this temperature and remained in water solution, but the maximal yield was obtained after a shorter reaction time at lower alkalinity. Although trehalose alone is stable at alkaline pH, extraction yields of trehalose from yeast decreased with increasing alkalinity. This finding led us to propose a two-step process in which trehalose is separated in the first step and ergosterol in the second. The possibility to apply this method to fractionate oleaginous microbes in process scale is discussed from technical viewpoints.