mRNA in situ hybridization is a standard laboratory technique for analyzing gene expression. In a small, transparent specimen like a zebrafish embryo, this technique is straightforward and works well. Cold Spring Harbor Protocols has a set of protocols (here, here and here) describing the method from Cecilia Moens. But what happens when you’re dealing with a larger, opaque zebrafish tissue like the adult brain? Unlike mammals, zebrafish exhibit intense ongoing neurogenesis in all areas of the central nervous system. Adult zebrafish are increasingly being used in behavioral studies as well. Because the number of antibodies useful for examining expression in zebrafish is limited, mRNA in situ hybridization is a vital tool for understanding what’s happening during these processes. In the February issue of Cold Spring Harbor Protocols, Reinhard Köster and colleagues from the Helmholtz Zentrum München provide an adaptation of the standard in situ method that deals with these larger, opaque tissues by staining them after vibratome sectioning, Analysis of Gene Expression by In Situ Hybridization on Adult Zebrafish Brain Sections. While the brain is used as the sample tissue in this protocol, it can easily be modified for analysis of other adult tissues.