Optimisation of drug carrier systems and drug delivery strategies that take into account the peculiarities of individual infectious agents and diseases are key elements of modern drug development. In the following, different aspects of a rational design for antiparasitic drug formulation will be reviewed, covering delivery systems such as nano- and microparticles, liposomes, emulsions and microemulsions, cochleates and bioadhesive macromolecules. Functional properties for each carrier system will be discussed as well as their therapeutic efficacy for parasitic diseases, including leishmaniasis, human African trypanosomiasis, human cryptosporidiosis, malaria and schistosomiasis. Critical issues for the application of drug carrier systems will be discussed, focusing on biopharmaceutical and pathophysiological parameters such as routes of application, improvement of body distribution and targeting intracellularly persisting pathogens.