Ether lipids were identified among components liberated with HF and nitrous acid deamination from Acanthamoeba rhysodes whole cells and its membrane glycoinositolphospholipids (GIPL). Liberated ether glycerols were converted to various derivatives that served characterization thereof. These included TMS and isopropylidene derivatives, oxidation with sodium periodate to aldehyde followed by reduction with NaBH4 to alcohol, and reaction of the alcohol with acetic anhydrite to form acetate derivatives. Periodate sensitivity demonstrated that the alkyl side chains were linked to the sn-1 position of glycerol. Combined information from TLC, GC–MS analysis, MALDI-TOF spectrometry, and chemical degradation experiments indicated the presence of ether-linked saturated normal and branched hydrocarbons with a length of C20–23 in the phospholipid fraction, C20–24 in free GPI, and C21–23 in the LPG polymer. The distribution of particular classes of alkylglycerols was similar for phospholipid and GPI fractions, and amounted to 2.62 % (±0.04–0.28) 1-O-eicosanyl-sn-glycerol, 16.66 % (±0.32–1.1) 1-O-uncosanyl-sn-glycerol, 9.18 % (±0.33–1.37) anteiso-1-O-docosanyl-sn-glycerol, 47.56 % (±0.32–2.14) 1-O-docosanyl-sn-glycerol, 20.56 % (±0.58–1.67) anteiso-1-O-tricosanyl-sn-glycerol, and 2.34 % (±0.12–0.63) 1-O-tricosanyl-sn-glycerol. For LPG preparation, the most abundant were anteiso-1-O-tricosanyl-sn-glycerol (57.26 %) and 1-O-docosanyl-sn-glycerol (30.12 %). The data from TLC and GC–MS analysis showed that ether lipids from phospholipids probably represent the lyso-alkylglycerol type, while those derived from GIPL are alkylacylglycerol moieties.