Complex emergencies emerged as a new type of disaster following the end of the Cold War, and have become increasingly common in recent years. Human activity including civil strife, war, and political repression often coexist with and contribute to natural phenomena such as famine. They frequently result in high mortality, population displacement, and the disruption of civil society and its infrastructure. This article reviews the context of recent complex emergencies, and their expected health consequences, such as diarrhea, measles, malnutrition and outbreaks of infectious disease, and the disruption of mechanisms of disease control and surveillance. However, the complex nature of these emergencies also may have unexpected consequences, such as hindering understanding of their causes or limiting the attention paid to them by the public. This paper discusses the context and consequences of complex emergencies from the health standpoint, and explores some of their unexpected effects.