Ether (phospho)lipids form a particular subgroup of phospholipids, whose characteristic feature is an ether bond at the sn-1 position of the glycerol backbone. Their biosynthesis involves the concerted action of peroxisomal and endoplasmic reticulum enzymes. An inborn deficiency of ether phospholipid biosynthesis has drastic consequences in humans causing the fatal disease rhizomelic chondrodysplasia punctata. In addition to intrinsic defects in the production of ether lipids, a depletion of all or some ether lipid species has been reported in a multitude of diseases but the significance of these findings is often unclear. Particularly, a role of a reduction of certain ether lipids in the etiology of Alzheimers disease is discussed. Several types of ether lipids exist covering many different functions across almost all living species. The most abundant subtype constitute the plasmalogens, which carry a vinyl ether bond as typical structural feature. These compounds are thought to have essential roles in membrane biology regulating fusion processes or shaping the biophysical properties of biomembranes. In addition, functions as antioxidants, in the generation of second messengers or in the storage of polyunsaturated fatty acids have been proposed, but many aspects of plasmalogen biology, particularly in the alive organism, are still enigmatic. In the present thesis, we investigated the significance of ether lipids for the mammalian nervous system using in vitro and in vivo models of ether lipid deficiency. Prompted by signs of pathologic hyperactivity in ether lipid-deficient mice, we examined neurotransmitter levels in these animals and detected ubiquitously decreased brain levels of different transmitter types. These changes were restricted to synapses, but were not caused by general synaptic loss. Instead, our data point towards a defect in the vesicular transport of neurotransmitters as the origin of the reduction of these compounds. At the murine neuromuscular junction, ether lipid deficiency led to an abnormal morphologic appearance and to abnormalities in synaptic transmission. Furthermore, our studies in the cardiac system of ether lipid-deficient mice corroborated the suggested association between congenital heart disease, in particular septal defects, and ether lipid deficiency and revealed impaired cardiac function in aged ether lipid-deficient mice. In a separate set of experiments, we analyzed the plasma levels of selected ether lipid species in a longitudinal study involving human subjects developing Alzheimers disease. Here, we found that the levels of some choline-containing species increased during the normal aging process, but were even more elevated in patients diagnosed with Alzheimers disease. Finally, by conducting a phospholipidome of human cells and animal tissue, we examined compensatory adaptations to the condition of ether lipid deficiency. Remarkably, the loss of ethanolamine plasmalogens was counteracted by increased levels of phosphatidylethanolamine ensuring a constant amount of ethanolamine phospholipids. At the same time, these compensatory mechanisms evoked a shift from species with omega-3 polyunsaturated fatty acids to such with omega-6 fatty acids. In total, our findings reveal new facets concerning the function of ether lipids in the mammalian body and underscore the importance of these compounds for the nervous system. Furthermore, the data bear interesting implications for diseases with reduced levels of ether lipids, particularly inborn deficiencies in ether lipid biosynthesis, but also more common diseases like Alzheimers disease or neurodevelopmental disorders. Our investigation of compensatory mechanisms exposes a remarkable adaptation of the phospholipid composition in response to altered levels of ether lipids, but points out that also the shift in fatty acid composition needs to be taken into account, when discussing pathological consequences of ether lipid deficiency.