Cyclin-dependent protein kinases (CDKs) are key regulators of the eukaryotic cell cycle and of the eukaryotic transcription machinery. Here, we report the characterisation of Pfcrk-3 (P. falciparum CDK-related kinase 3, PlasmoDB identifier PFD0740w), an unusually large CDK-related protein whose kinase domain displays maximal homology to those CDKs which are, in other eukaryotes, involved in the control of transcription. The closest enzyme in yeast is BUR1 ("Bypass Upstream activating sequence Requirement"), known to control gene expression through interaction with chromatin modification enzymes. Consistent with this, immunofluorescence data show that Pfcrk-3 colocalises with histones. We show that recombinant Pfcrk-3 associates with histone H1 kinase activity in parasite extracts, and that this association is detectable even if the catalytic domain of Pfcrk-3 is rendered inactive by site-directed mutagenesis, indicating that Pfcrk-3 is part of a complex that includes other protein kinases. Immunoprecipitates obtained from extracts of transgenic parasites expressing HA-tagged Pfcrk-3 using a hemagglutinin (HA) antibody displayed both protein kinase and histone deacetylase activities. Reverse genetics data show that the pfcrk-3 locus can be targeted only if the genetic modification does not cause loss-of-function. Taken together, our data strongly suggests that Pfcrk-3 fulfils a crucial role in the intraerythrocytic development of P. falciparum, presumably through chromatin modification-dependent regulation of gene expression.