OBJECTIVE: To describe the factors associated with malaria infection and anaemia in pregnancy in northern Ghana. METHOD: We studied 3642 pregnant women of all gravidities and gestational age of 18-32 weeks who attended an antenatal clinic in the Kassena-Nankana district of Ghana between June 2004 and July 2006. Blood samples were examined for haemoglobin concentrations and parasitaemia, and we obtained socio-demographic data, an obstetric history, information on their past and current state of health and bed net use. RESULTS: The overall prevalence of malaria parasitaemia during pregnancy was 47%. Older age [adjusted odds ratio (AOR) 0.65, 95% CI 0.54-0.78], multigravidity (AOR 0.51, 95% CI 0.42-0.61) and third trimester of pregnancy (AOR 0.85, 95% CI 0.73-0.99) were associated with a decreased risk of parasitaemia. Enrollment during the rainy or post-rainy season was associated with an increased risk of parasitaemia (AOR 2.59, 95% CI 2.20-3.04 and AOR 3.12, 95% CI, 2.60-3.74 respectively). Malaria infection was associated with an increased risk of anaemia among young women. The prevalences of anaemia (Hb<11.0 g/dl) and severe anaemia (Hb<7.0 g/dl) during pregnancy were 72% and 2% respectively. The risk of anaemia was lower in older women (AOR 0.79, 95% CI, 0.64-0.97), multigravidae (AOR 0.67, 95% CI 0.55-0.83) and in educated women (AOR 0.81, 0.68-0.98). CONCLUSION: The prevalence of malaria parasitaemia and anaemia among pregnant women in Kassena-Nankana district is high with marked seasonal variation. Targeting of interventions to the high transmission season and to paucigravidae may be appropriate in this setting.