The study investigated the role of climatic variables and irrigated agricultural on the seasonality of malaria transmission in New Halfa, eastern Sudan. A time-series analysis was performed using monthly climatic variables, monthly water available for irrigation of crops and monthly slide positive rate of malaria during the period 1986-2002. Cases of malaria were reported every month of the year with a mean of 13.0/100 persons/month (95% CI: 11.9-14.2), and bimodal annual pattern in autumn and winter seasons. Rainfall was the significant climatic variable in the transmission of the disease, whereas heavy rainfall was found to initiate epidemics. Temperature, relative humidity and irrigation water were not significant factors.