Complex emergencies are situations of violence, nutritional insecurity and population displacement of increasing frequency and intensity which pose a serious public health problem to the affected populations. Communicable diseases, especially waterborne diseases as cholera, cause up to 75% of morbidity and mortality in complex emergencies. The objective is to analyze the cholera epidemics in complex emergencies and cholera risk factors associated with the emergency. This descriptive study analyzes cholera epidemics in complex emergencies in affected countries between 2000 and 2011 by reviewing the information formally published and unpublished reports from field organizations and aid agencies. Indicators of incidence, mortality and case-fatality were used. The mean annual incidence of cholera in areas of complex emergency was 1.2 per 1,000 population (95% CI = 0.5 to 1.9) and the average fatality of epidemics was 4.08% (95% CI = 3.3 to 4.86). In the cases studied the following specific risk factors of complex emergencies are present and amplify the impacts of cholera: serious deficiencies in water and sanitation, over-crowding, weak health system, lack of previous immunity of the affected population and introduction or reintroduction of causative agent.