Both malaria and anaemia have adverse effects on maternal and perinatal outcomes. Thus there is an urgent need to investigate the co-epidemiology of malaria and anaemia and their combined impact on maternal and perinatal outcomes in the different regions of Sudan. Various cross-sectional and case control studies conducted during the years 2003-2010 to investigate the epidemiology of malaria and anaemia and their impact on maternal and perinatal outcomes in different regions of Sudan were compared. While 13.7% of antenatal attendants in New Halfa had peripheral microscopically detected Plasmodium falciparum malaria, placental malaria (using histological examinations) was prevalent in 32.0-40% and 19.5% of parturient women in New Halfa and Gadarif Hospitals, respectively. Malaria was a risk factor for anaemia in New Halfa and for stillbirths in Omdurman Maternity Hospital. Anaemia was present in 52.5%, 62.6% and 80.2% of pregnant women in Medani, New Halfa, and Gadarif Hospitals, respectively. In Gadarif, 57.3% of pregnant women had a folate deficiency, while 1% had a vitamin B12, deficiency. In Medani, zinc and copper deficiencies were detected in 45.0% and 4% of pregnant women, respectively. Anaemia was a risk factor for low birth weight in Al-Fashir, for fetal anaemia in New Halfa, and for stillbirth in Kassala Hospital. More care should be taken to ensure proper nutrition and malaria prevention such as bed nets and intermittent preventive treatments to avoid these diseases and their effects on maternal and perinatal outcomes.