Protozoan parasites, such as those responsible for malaria and African Sleeping Sickness, represent a huge burden to the developing world. Current chemotherapy to combat these diseases is inadequate: antiquated, toxic and increasingly ineffective due to drug resistance. In this article, the potential usefulness of targeting key regulators of the parasite cell cycle will be discussed, paying particular attention to three families of protein kinases: Cyclin-dependent kinases, glycogen synthase kinases and Aurora kinases. This review shall outline their identification, which has been greatly accelerated by the availability of parasite genome data, their validation as bona fide regulators of the parasite cell cycle and current data on the availability and anti-parasite activity of inhibitors.