Synthetic antisense oligodeoxynucleotides can inhibit the expression of a gene in a sequence-specific manner at the translational level. Their potential use to understand the role of neuropeptides or neurotransmitters in neuroendocrine and behavioral functions, and perhaps for therapeutic gene suppression, has become of great interest in neuroscience, especially in the cases of absence of available specific antagonists. Whether their action can be fully specific to the target gene and not only sequence-specific is, however, the main question about their application to brain studies. A number of factors such as the mode of action, specificity and chemistry of antisense molecules as well as the carrier vehicle and the time course of antisense treatment, must be carefully considered for the design and successful application of antisense oligonucleotides. Assay systems and controls must be chosen so as to ensure that the observed biological effects of antisense oligodeoxynucleotides do in fact reflect the result of a specific target gene inhibition. This article discusses these biochemical factors with the emphasis on the use of phosphodiester or phosphorothioate oligodeoxynucleotides in neuroendocrine or behavioral studies.