The RNase protection assay is a standard approach to determine mRNA levels of a gene of interest in different tissues, developmental stages, or times of the day. Splicing or promoter variants can be studied with specific probes. It is widely used in chronobiology to study the temporal profile of expression of circadian genes and the effects of genetic manipulation on these oscillations. Methods to generate the riboprobes and to perform the RNase protection assay itself are described in this chapter.