This study compares the mRNA expression pattern for the three glutamate transporters EAAC1, GLT1 and GLAST in rat brain, using a sensitive non-radioactive in situ hybridization technique. The results confirm the predominantly neuronal localization of EAAC1 mRNA, the astroglial and ependymal localization of GLAST mRNA and the astroglial and neuronal localization of GLT1 mRNA. Further, we demonstrate, using a novel differential double hybridization protocol, that the presence of GLT1 mRNA in neurons is more widespread than previously thought, and that it encompasses the majority of neurons in the neocortex, neurons in the external plexiform layer in the olfactory bulb, neurons in dorsal and ventral parts of the anterior olfactory nucleus, the majority of neurons in the anteromedial thalamic nuclei, the CA3 pyramidal neurons in the hippocampus and neurons in the inferior olive. In addition, we demonstrate marked variations in the expression levels of GLT1 and GLAST mRNAs in different brain areas, suggesting that their mRNA levels are regulated by different mechanisms. Finally, for EAAC1 we demonstrate also a widespread distribution and a marked heterogeneity in the expression levels. EAAC1 is strongly expressed by a heretofore unrecognized group of cells in white matter tracts such as the corpus callosum, fimbria-fornix or anterior commissure. Also, strong EAAC1 expression is present in groups of scattered cells in grey matter areas of much of the forebrain and the cerebellum. These results provide more detailed information about the precise cellular localization of these three glutamate transporters and their regulation at the mRNA level.