Population effects of malaria vaccination programs will depend on a complex interaction of the stage specificity of the vaccine, its duration of effectiveness, whether it is responsive to natural boosting, the strategy implemented, the proportion vaccinated and the pre-existing endemic conditions. In this article, Elizabeth Halloran and Claudio Struchiner review models of malaria transmission that incorporate aspects of immunity relevant to studying the effects of stage-specific malaria vaccination programs. They discuss the difference in the assumptions and applicability of the models and compare their predictions. Experience with malaria has demonstrated the difficulty in eliminating transmission, so emphasis needs to be on the new host-parasite balance that will be induced by the vaccination program. Although Halloran and Struchiner advise caution in interpreting the results of such models, they conclude that quantitative and theoretical analysis will be important in planning and evaluating interventions with malaria vaccines.