In situ hybridization to mRNA in embryo sections or wholemount embryos is o
ne of the most powerful analytical tools available to the molecular develop
mental biologist. For many workers, this procedure provides the first insig
hts into the function of newly isolated genes, allowing the formulation of
hypotheses and setting the course for further research. This paper presents
a personal historical perspective of the development of in situ hybridizat
ion, looks at the theory and practice of the technique, summarizes the curr
ent state of the art, and speculates on possible directions for the future
as a tool in functional genomics.