Strokes are a critical problem in the U.S. that affect more than 500 000 people annually. Research into the causes of stroke and testing of drug therapies to reduce ischemic and postischemic damage to the brain is frustrated by an inability to continuously follow the physical and chemical events that occur during ischemia and reperfusion in vivo. Near-IR spectrometry is used in this paper to observe stroke-induced changes in the lipids and proteins of whole brain samples and in intact subjects. The examination of whole brains is made possible by a combination of hardware and software techniques designed to make the sample presentation to the spectrometer more reproducible. Near-IR spectrophotometry of brain tissue discriminates between adult (3-4 months of age) and aged (18-20 months of age) brains as well as between brains exposed to 5- and 10-min ischemia. The near-IR analytical method has many applications in aging and stroke research, including the noninvasive determination of age from brain spectra obtained transcranially, simultaneous multicomponent analysis of lipids and proteins, and quantification of edema.