A nonaqueous capillary electrophoresis method with electrospray-mass spectrometric detection was developed to study the glycerophospholipid fraction in olive fruit and olive oil samples. In olive fruits, where the information available about the phospholipid fraction was very scarce, results obtained in this work allowed us to complete and improve this knowledge. The glycerophospholipid fraction of the olive fruit samples analyzed was composed of phosphatidylcholine (PC), phosphatidylethanolamine (PE), lysophosphatidylethanolamine (lyso-PE), phosphatidylinositol (PI), phosphatidic acid (PA), lysophosphatidic acid (lyso-PA), and phosphatidylglycerol (PG). Differences in the relative abundance of the glycerophospholipid classes determined were observed as a function of the botanical and geographical origin of the olive fruits analyzed. Interestingly, the olive stone and pulp analyzed also showed different glycerophospholipid compositions. For olive oil, five glycerophospholipids (lyso-PA, PC, PE, lyso-PE, and PG) were detected. Finally, identification of the main molecular species in the different glycerophospholipid classes for the olive fruit samples analyzed was accomplished by tandem mass spectrometric experiments and information from the literature.