Background: Cholera epidemics have a recorded history in eastern Congo dating to 1971. A study was conducted to find out the linkage between climate variability/change and cholera outbreak and to assess the related economic cost in the management of cholera in Congo. Methods: This study integrates historical data (20 years) on temperature and rainfall with the burden of disease from cholera in South-Kivu province, eastern Congo. Results: Analyses of precipitation and temperatures characteristics in South-Kivu provinces showed that cholera epidemics are closely associated with climatic factors variability. Peaks in Cholera new cases were in synchrony with peaks in rainfalls. Cholera infection cases declined significantly (P<0.05) with the rise in the average temperature. The monthly number of new Cholera cases oscillated between 5 and 450. For every rise of the average temperature by 0.35 degrees C to 0.75 degrees C degree Celsius, and for every change in the rainfall variability by 10-19%, it is likely cholera infection risks will increase by 17 to 25%. The medical cost of treatment of Cholera case infection was found to be of US$50 to 250 per capita. The total costs of Cholera attributable to climate change were found to fall in the range of 4 to 8% of the per capita in annual income in Bukavu town. Conclusion: It is likely that high rainfall favor multiplication of the bacteria and contamination of water sources by the bacteria (Vibrio cholerae). The consumption of polluted water, promiscuity, population density and lack of hygiene are determinants favoring spread and infection of the bacteria among human beings living in over-crowded environments.