As a prerequisite for blocking specific gene expression in the brain, the pharmacokinetics of two radiolabelled analogs of antisense oligodeoxyribonucleotides (unmodified O-ODN and nuclease resistant phosphorothioate S-ODN) were examined by infusion into the baso-lateral nucleus of amygdala. Both ODN analogs were found to penetrate at restricted distances into the brain tissue. Rapidly after injection, O-ODN was almost completely degraded, while S-ODN remained intact up to 24 h following administration as examined by gel electrophoresis of nucleic acids recovered from the injection site. The tissue clearance of the radioactivity delivered in a form of O-ODN and S-ODN was also different, the former characterized by much better tissue retention. Microscopic studies suggested that S-ODN can apparently penetrate across the cell membrane and accumulate both in the cytoplasm in the cell nucleus. In situ hybridisation histochemistry experiments (antisense probe to injected ODN) revealed that injected S-ODN was present in a form available for annealing with the complementary strand. Our results provide a basic description of the distribution, retention, and stability of antisense oligonucleotides injected into brain tissue.