The apical organelles are characteristic secretory vesicles of Plasmodium, Toxoplasma, Cryptosporidium and other apicomplexan organisms. They consist of rhoptries, micronemes and dense granules. Recent research has provided much new data concerning their structure, contents, functions and development. All of these organelles contain complex mixtures of proteins, with broad homologies as well as differences in molecular structure between species and genera. Many of the proteins interact with host cell membranes, and are thought to mediate selective adhesion to host cells as well as membrane modification during intracellular invasion. Micronemal proteins are important in the initial selection of host cells, and in enabling gliding motility of the parasites, while rhoptries appear to be more important in parasitophorous vacuole formation. Dense granules are involved predominantly in modifying the host cell after invasion. Research into apical organellar composition and function depends on accurate assignment of molecular identity. This requires the simultaneous application of several complementary approaches including immunolocalisation by light- and electron-microscopy, subcellular fractionation, and transgene expression. The merits and limitations of these different types of approach are discussed, and the importance of cell fractionation methods in characterising apical organelle proteins is stressed.