An experimental method and its associated mathematical model are described to quantitate in vivo incorporation rates into and turnovers of fatty acids (FAs) within stable brain metabolic compartments, particularly phospholipids. A radiolabeled FA is injected i.v. in a rat, and arterial plasma unacylated FA radioactivities and unlabeled concentrations are sampled until the animal is killed after 15 min, when the brain is analyzed biochemically or with quantitative autoradiography. Unbound unacylated label in blood easily crosses the blood-brain barrier; rapidly equilibrates in the unacylated FA, acyl-CoA and phosphatidate-diacylglycerol brain pools; then is incorporated into phospholipids and other stable metabolic compartments. Uptake and incorporation of labeled FAs are independent of cerebral blood flow at constant brain blood volume. Different labeled FAs enter specific sn positions of different brain phospholipids, suggesting that a combination of probes can be used to investigate metabolism of these phospholipids. Thus, [9,10-3-H]palmitate preferentially labels the sn1 position of phosphatidylcholine; [1-14C]arachidonate the sn2 positions of phosphatidylinositol and phosphatidylcholine; and [1-14C]docosahexaenoate the sn2 positions of phosphatidylethanolamine and phosphatidylcholine. The FA model provides an operational equation for rates of incorporation of FAs into brain phospholipids, taking into account intracerebral recycling and de novo synthesis of the FA, as well as entry into brain of FA from acylated blood sources. The equation is essentially independent of specific details of the proposed model, and can be used to calculate turnovers and half-lives of FAs within different phospholipid classes. For the model to be most applicable, experiments should satisfy conditions for pulse-labeling of the phospholipids, with brain sampling times short enough to minimize exchange of label between stable metabolic compartments. A 15-20 min sampling time satisfies these criteria. The FA method has been used to elucidate the dynamics of brain phospholipids metabolism in relation to brain development, brain tumor, chronically reduced auditory input, transient ischemic insult, axotomy with and without nerve regeneration, and cholinergic stimulation in animals with or without a chronic unilateral lesion of the nucleus basalis magnocellularis.