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Malaria is one of the most important health problems in Sudan. The current study confirmed precious findings of presence of correlations between malaria disease and the different climatic factors (rainfall, relative humidity, and temperature). Three areas were studied; they were quite different in their ecology and consequently in the livelihoods practiced by the inhabitants. In Central Sudan (Sennar) the high peak of the disease was found to occur during autumn and winter and that was found to correlate significantly with the rainfall and percent of relative humidity. In Northern Sudan (Dongola) the proportion of the disease was found to correlate significantly with temperature only, however, no differences were found between seasons. That was expected as the northern state is very arid (desert) and its average rainfall doesn’t exceed 75 mm/ year and the seasonal variation in humidity range between 17-26%. In western Sudan (Elobied), in spite of the fact that it is more humid than Northern Sudan, no significant seasonal trend was found and the temperature was not found to significantly affect the proportion of the disease. Western Sudan in general is characterised by acute water shortage and accordingly the citizens use different methods (ponds, barrels etc.) for water storage all the year around which was found to provide suitable environment for reproduction of mosquito and accordingly was found to cause increase in incidents of malaria epidemics. The relationship between the climatic factors and the proportion of the disease was found to be offset by the availability of stored water not only in western Sudan but also in many different parts of the country.