Diminished levels of docosahexaenoic acid (22:6n-3), the major fatty acid (FA) synthesized from alpha-linolenic acid (18:3n-3), have been implicated in functional impairment in the developing and adult brain. We have now examined the changes in phospholipid (PL) molecular species in the developing postnatal cortex, a region recently shown to be affected by a robust aberration in neuronal cell migration, after maternal diet alpha-linolenic acid deprivation (Yavin et al. (2009)Neuroscience162(4),1011). The frontal cortex PL composition of 1- to 4-week-old rats was analyzed by gas chromatography and electrospray ionization/tandem mass spectrometry. Changes in the cortical PL molecular species profile by dietary means appear very specific as 22:6n-3 was exclusively substituted by docosapentaenoic acid (22:5n-6). However, molecular species were conserved with respect to the combination of specific polar head groups (i.e. ethanolamine and serine) in sn-3 and defined saturated/mono-unsaturated FA in sn-1 position even when the sn-2 FA moiety underwent diet-induced changes. Our results suggest that substitution of docosahexaenoic acid by docosapentaenoic acid is tightly regulated presumably to maintain a proper biophysical characteristic of membrane PL molecular species. The importance of this conservation may underscore the possible biochemical consequences of this substitution in regulating certain functions in the developing brain.