A cross-sectional community-based study was carried out in Khartoum urban area aimed at stratifying the area by risk of malaria transmission. Two thousand households [8092 individuals] were surveyed during the cold, dry and rainy seasons of 2002. Households with screened windows, using bednets or both were 5.0% [95% CI: 4.1-6.0], 10.9% [95% CI: 9.5-12.3] and 1.8% [95% CI: 1.2-2.5] respectively. Access to health services was high. Only 3.8% [95% CI: 2.9-4.7] of households kept antimalarial drugs at home. The parasite rate, spleen rate and fever rate were very low [0.21%, 0.17% and 0.97% respectively]. Overall, people in Greater Bahry suffer a greater burden of malaria than those in Greater Khartoum or Greater Omdurman, with a seasonal pattern of transmission.