Molecular biology is providing powerful tools for cloning and sequencing genes. The more difficult task is that of ascribing functions to the specific DNA sequences that appear to code for proteins, the “open reading frames,” or of regulating the expression of known genes in biological systems in order to determine their contributions to cellular functions. The classical genetic approach of making mutants is difficult in eukaryotic systems, with the exception of yeasts and viruses, and has proved of limited utility. A promising approach to this problem has been to introduce into either the in vitro assay or tissue culture system oligodeoxyribonucleotides with nucleotide sequences complementary to the protein coding or “sense” sequence, usually referred to as “antisense” oligonucleotides. The term MATAGEN (MAsking TApe for Gene ExpressioN) has also been used for these compounds, which appear to inhibit gene expression predominantly by hybridization arrest of translation. Interest in the use of antisense molecules for the study of gene expression and regulation has increased dramatically in the past few years. The demonstrated utility of the antisense oligomer in both in vitro and tissue culture assays, the increased availability of nucleotide sequence data as well as improvements in nucleic acid sequencing techniques, and the automation of synthetic procedures for their preparation have made studies using these molecules more practical. This review focuses on short oligodeoxyribonucleotides, which offer important stability and synthetic advantages over the use of antisense RNA transcripts, and is intended as an introduction to practical approaches in the use of antisense oligodeoxyribonucleotides in biological systems. For synthetic techniques, the reader is referred to the individual references cited.