Chemically-modified oligonucleotides are now routinely used to prevent gene expression in cell-free media and in cultured cells. The binding of an antisense sequence to a complementary RNA target may lead to the selective inhibition of the encoded information. This may occur at different levels: splicing; transport of the mature RNA from the nucleus to the cytoplasm; translation. Antisense oligonucleotides constitute an interesting tool to shed some light on gene function. They are also potential new therapeutic agents against pathogenic organisms. This review discusses the rules that guide the design of an antisense oligomer and the choice of a target sequence. Examples of the potential use of antisense oligonucleotides in the fields of virology and parasitology, in particular in relation to trypanosomatids, are described.