It appears that the application of antisense nucleic acids to drug development and gene function analysis are now established fields, and success in the use of antisense molecules has increased over recent years through modulating chemical and biological properties of oligonucleotides via the specific chemistry employed in their construction. In contrast, the targets of antisense nucleic acids are unchangeable RNA molecules, each with a defined strcuture. The local properties of the target represent a major limitation of the effectiveness of complementary nucleic acid inhibitors, and as such the search for appropriate local target sites for the invasion of an antisense strand is the focus of current research. Here, recent developments in the study of target structures and their accessibility for antisense nucleic acids, as well as concepts for their analysis, will be summarized.