The fate of 15-mer phosphorothioate-modified antisense oligonucleotides to c-fos was followed after their microinjection into rat brain. Using radiolabeled oligonucleotides, it was demonstrated that the bulk of the material stays in the injected region but that a minor part is transported with the projection pathways to regions far away from the site of injection. Using tetramethylrhodamine-isothiocyanate (TRITC) labeling as well as fluorescein isothiocyanate (FITC) labeling, it was found that the oligonucleotides were taken up by a great number of cells within 30 minutes after the injection. A diffuse cytoplasmic staining and also nuclear staining were observed in these cells, which could be identified exclusively as neurons by double labeling for the neuron-specific protein NeuN. At later times (6, 24, and 48 hours), the appearance of the oligonucleotides changed gradually to a punctate cytoplasmic staining, which by electron microscopic analysis was shown to be caused by the presence of the oligonucleotides in intracellular vesicles. The pattern of intracellular fluorescence was changed when the oligonucleotides were injected together with the cationic lipid 1,2-bis(oleoyloxy)-3-(trimethylammonio)propane (DOTAP). A small number of astrocytes and microglial cells were found to be labeled by the oligonucleotides, but only at later times after the injection and exclusively in a punctate cytoplasmic manner. Thus, the uptake of oligonucleotides in the nerve and glial cell populations of the brain might involve different mechanisms, the one in the neurons appearing to be very rapid and potent.