Methods for producing lipids from lignocellulosic biomass are provided. Sugars produced by pretreatment of lignocellulosic biomass are utilized by heterotrophic oleaginous fungi or yeast to increase their biomass and to produce lipids without prior detoxification of the pretreated biomass. After the fungi/yeast are cultured with the sugars, solid residues from the pretreated biomass are combined with the fungi/yeast under conditions which allow simultaneous 1) enzymatic degradation of cellulose and/or hemicellulose to produce sugars and 2) fermentation of the sugars for further increases in biomass and lipid production.