Mitogen-activated protein kinases (MAPKs) are serine/threonine kinases that have an important role in signal transduction. Extracellular signal-regulated kinase 3 (ERK3), also known as MAPK6, is an atypical MAPK. Here, we describe in detail an in vitro assay for the kinase activity of ERK3 using myelin basic protein (MBP) or steroid receptor coactivator-3 (SRC-3) as substrates. The assay is carried out in the presence of [y-32P]-ATP which results in radiolabeling of phosphorylated substrates. Separation of the reaction components by gel electrophoresis followed by autoradiography enables detection of the radiolabeled products, and hence determination of the kinase activity of ERK3. This assay can be used for several applications including identification of substrates, determination of the effect of molecules or mutations on kinase activity, and testing specific kinase inhibitors. Furthermore, the protocol outlined here can be adapted to measure the activity of other kinases by using their specific substrates.