The first three introns of CRK2, a cdc2-homologous gene, have been compared in a total of seven Plasmodium species. The introns were located at conserved sites, suggesting an ancestral origin. Interspecific comparison of intron sequences agreed with the previously inferred evolutionary relationships of the malaria parasites. Unlike the introns in the rodent malaria species, the similarity of the CRK2 introns was regionalized between the human parasite P. vivax and the simian parasite P. knowlesi: the central region of all three introns showed markedly less interspecific similarity than the 5′ and 3′ regions. This was also in contrast with the organisation and composition of homologous intron pairs from other genes of the same two species. No conservation at the level of secondary strucure could be detected, even between highly similar introns. A database search for intron-containing Plasmodium genes was performed. All introns obtained in this way plus the additional CRK2 introns were scanned for the presence of putative branching site consensus sequences. For P. falciparum, we present an update of the 5′ and 3′ splice-site consensus.