Cell division and proliferation of all eukaryotics must follow a genetic program, termed the cell cycle. To ensure proper progression through the cell cycle, proteins that are intimately involved in its regulation must be periodically expressed within an appropriate window of the cycle. Cyclin and cyclin-dependent kinases are the modular components of the core clock machinery of the cell cycle. Progression through the cell cycle requires the activation of Cdks. The activities of these classes of kinases are tightly regulated by both positive and negative factors, and most importantly perturbation of Cdk activities can result in tumorigenesis. Progress has been made recently in connecting specific cyclin-Cdk kinase complexes and transcription. It is still unclear how cyclin/Cdk complexes regulate transcription, and most importantly what their substrates are. The aim of this review is to discuss our current understanding of the molecular mechanisms underlying the transcription properties of defined cyclin-dependent kinases, with a particular emphasis on the cyclin T/Cdk9 (P-TEFb) complex, and its role in the regulation of cell cycle controlling genes.