The effects of various chemical extraction procedures on the determination of lipid composition of rat and mouse brain have been investigated. Tissue extractions with formic acid/acetone or perchloric acid both resulted in significant losses of total phospholipids and cholesterol. Perchloric acid extraction also degraded, almost quantitatively, ethanolamine plasmalogens to lysophosphatidylethanolamine. Our findings have thus demonstrated that conventional procedures used for extraction of brain tissue for analysis of choline and acetylcholine content cannot also be used for concurrent/simultaneous extraction of phospholipids and cholesterol from the same tissue.