Analysis and quantification of ether-lipid phospholipid species―also known as plasmalogens―is a crucial step in the study of the biological functions played by these lipids. Application of analytical separation methods and high-resolution mass spectrometry has gained much attention in this regard, while resolution issues and time-consuming sequences interfered with these advances. Herein, we describe a simple and rapid method for the analysis of plasmalogen (Pl) species by HILIC-HRMS. This method is able to identify and quantify relative levels of ethanolamine-plasmalogens (PlsEtn) and choline-plasmalogens (PlsCho) in biological matrices such as whole blood, plasma, erythrocytes, and also retina. Moreover, we provide a detailed and modified lipid extraction method that is applicable to almost all biological matrices.