The changes in guinea pig brain (cerebrum) glycerophospholipid molecular species resulting from a low α-linolenic acid (ALA) diet are described. Two groups of six guinea pigs were raised from birth to 16 wk of age on either an n-3 deficient diet containing 0.01 g ALA/100 g diet or n-3 sufficient diet containing 0.71 g ALA/100 g diet. Molecular species of diradyl glycerophosphoethanolamine (GroPEtn), glycerophosphocholine, glycerophosphoserine, and glycerophosphoinositol were analyzed by high-performance liquid chromatography with on-line electrospray ionization mass spectrometry (HPLC/ESI/MS). Alkenylacyl GroPEtn species were determined by comparing spectra before and after mild acid treatment while diacyl- and alkylacyl species were distinguished by HPLC/ESI/MS. The proportions of phospholipid classes and of the diradyl GroPEtn subclasses were not altered by diet changes. The main polyunsaturated molecular species of diradyl GroPEtn subclasses and of phosphatidylcholine and phosphatidylserine (PtdSer) contained 16:0, 18:0, or 18:1 in combination with docosahexaenoic acid (DHA, 22:6n-3), docosapentaenoic (DPA, 22:5n-6), or arachidonic acid (ARA, 20:4n-6). A significant proportion of DPA containing species were present in both diet groups, but in n-3 fatty acid deficiency, the proportion of DPA increased and DHA was primarily replaced by DPA. The combined value of main DHA and DPA containing species in the n-3 deficient group ranged from 91-111% when compared with the n-3 sufficient group, indicating a nearly quantitative replacement. The n-3 fatty acid deficiency did not lower the content of ARA containing molecular species of PtdSer of the guinea pig brain as reported previously for the rat brain. The molecular species of phosphatidylinositol were not altered by n-3 fatty acid deficiency. The present data show that the main consequence of a low ALA diet is the preferential replacement of DHA-containing molecular species by DPA-containing molecular species in alkenylacyl- and diacyl GroPEtn and PtdSer of guinea pig brain.