The ubiquitously expressed cyclin-dependent kinase 5 (cdk5) is essential for brain development. Bioactivation of cdk5 in the brain requires the presence of one of two related regulatory subunits, p35 and p39. Since either protein alone can activate cdk5, the significance of their coexistence as cdk5 kinase activators is unclear. To determine whether the two activators are expressed in different cells throughout the nervous system and during development, we compared the tissue distributions of cdk5, p35, and p39 mRNAs in the rat using in situ hybridization. In the adult rat, expression levels of p35 mRNA are generally higher in the brain than in the spinal cord, while the converse is observed for p39 mRNA. During neurogenesis, both p35 and p39 transcripts can be detected as early as embryonic day 12 (E12) in the marginal zone, but are absent from the ventricular zone, which may restrict cdk5 activation to the postmitotic neural cells in the developing brain. The expression levels of p35 and p39 mRNAs in the marginal zone increase by E15 and E17, paralleling the neurogenetic timetable. One exception is in the rostral forebrain, where p35 mRNA expression levels are high, suggesting that p35 may be the major activator for cdk5 during telencephalic morphogenesis. A significant level of p35 mRNA is present in the myotome at E12 and p35 expression persists in the premuscle mass and mature musculature at later stages, suggesting that p35 may also activate cdk5 during myogenesis.