All drugs used for malaria prophylaxis have common adverse effects, in addition to rare and/or severe adverse effects. For many of the drugs in current use, the common adverse effects include neuropsychiatric harms. This property makes these drugs unpopular with tourists and business travellers, most of whom will be well at the start of chemoprophylaxis. Drugs available to prevent malaria have not been rigorously researched in terms of the phenomenology of their unwanted effects. Consequently, prescribers are not well placed to give useful information to travellers on the incidence, natural history and avoidability of the harms they may experience from malaria chemoprophylaxis. There is some evidence that the adverse effects of mefloquine may be a post-hepatic syndrome caused by drug-induced liver damage with, in some users, symptomatic thyroid disturbance. However, confusion in the interpretation of the scientific evidence has led to conflicting messages regarding the safety of mefloquine and other antimalaria drugs, and to incorrect self-therapy by individual travellers, sometimes with fatal outcomes. In this review, the existing knowledge base for the safety of drugs currently used to prevent malaria is described along with present designs for future studies that would allow a rigorous safety assessment of candidate chemoprophylactic agents and of new drugs introduced to prevent malaria. There is an urgent need for internationally-agreed, evidence-based malaria prevention guidelines. These guidelines should be explicitly linked to the best available research evidence (normally systematic reviews of trials and individual randomised trials) and should highlight gaps in the knowledge base as priority areas for research.