As countries move to malaria elimination there are profound changes at the population level with both positive and negative implications. First, the gains of elimination are often seen primarily in terms of reductions in malarial disease although there has long been the suggestion that removal of vaguely defined malaria induced ‘immune suppression’ may confer other health benefits. A number of recent findings strongly support this; first the observation that sickle cell trait, long known to protect against malaria, confers protection against bacteraemia allowed a Mendelian randomisation approach to demonstrate that malaria directly leads to a large burden of severe bacterial disease which is reduced as malaria transmission reduces. This is supported by major reductions in childhood mortality associated with time limited antimalarial interventions. On the less positive side, reductions in malaria transmission lead to reductions in antimalarial immunity rendering populations susceptible to more severe disease should there be any rebound in transmission. The dynamics of this are complex and involve two different phenomena: the gradual accumulation of a birth cohort no longer exposed to malaria and the possible waning of established immunity in older members of the population.