Cultured brain cells oxidize glucose and numerous alternate substrates to CO2 for energy production, however, the importance of these observations to the intact brain have not been established. We have adapted in vivo brain microdialysis procedures to measure the rate of 14CO2 formation from 14C-glutamate, 14C-glutamine, and 14C-glucose in the hippocampus of awake unanesthetized free-moving rats. Two, 9 and 16 days after surgery (to implant guide cannulae) microdialysis probes were inserted into the guide cannulae and perfused with artificial CSF containing either 14C-glutamate, 14C-glutamine or 14C-glucose. Dialysate fractions were collected during 20 min intervals for determination of 14CO2. The amount of labelled 14CO2 increased for 40 to 60 min and then plateaued and remained relatively constant for at least 6 hours. When the probe was removed from the hippocampus and inserted into a vial containing non-radioactive CSF, 14CO2 production dropped rapidly. The quantity of 14CO2 recovered from glutamate was greater than from glucose or glutamine reflecting pool sizes, uptake characteristics and point of entry into oxidative pathways. The microdialysis system was verified by using model systems with cultured astrocytes suspended in media to simulate the brain. The present results indicate brain microdialysis may be used to study the role of alternate substrates in specific brain regions under varying physiological states.