While basic guidelines on HIV prevention in emergencies have been available for several years, international agencies involved in the provision of health services have not placed sufficient priority on the prevention of the human immune deficiency virus (HIV) and other sexually transmitted infections (STIs) in complex emergencies. This paper reviews the factors that may increase the risk of HIV transmission in populations affected by complex emergencies and outlines recommendations for research and programmes. Research into the most appropriate methods of carrying out HIV surveillance and interventions in these settings is needed. In the post-emergency phase programmes need to be far more extensive than those offered under the Minimal Initial Services Package (MISP). While the potential for stigmatization represents an important constraint, there is a need to prioritize HIV/STI interventions in order to prevent HIV transmission in emergency-affected populations themselves, as well as to contribute to regional control of the epidemic.