In sub-Saharan Africa, anaemia in pregnancy results from multiple causes including malaria, iron deficiency and haemoglobinopathies. In a cross-sectional study among 530 pregnant women in Ghana in November-December 1998, red blood cell indices were analysed with respect to malaria, serum concentrations of ferritin and C-reactive protein (CRP), and the haemoglobin and alpha-globin genotypes. Anaemia (haemoglobin [Hb] < 11 g/dL) was found in 54% of the women; 63% harboured malaria parasites at predominantly low numbers. Ferritin levels were considerably influenced by malaria and inflammatory processes (CRP > 0.6 mg/dL). Depending on the definition applied, the prevalence of iron deficiency ranged between 5% and 46%. The HbAS trait was observed in 14%, HbAC and elevated HbF in 7% each, and sickle cell disease in 1%. Heterozygous beta-thalassaemia was present in 1% of the women and alpha(+)-thalassaemia in 33% (29% heterozygous, 4% homozygous). Women with HbAS had higher malaria parasite densities than those with HbAA. In individuals with highly elevated HbF (> 10%), parasitaemia occurred in 27% only. Low gravidity, second trimester of pregnancy, malaria, raised CRP levels, and homozygous alpha(+)-thalassaemia were independent risk factors for anaemia in multivariate analysis. alpha(+)-Thalassaemia, however, was associated with a lesser degree of malarial anaemia when compared to non-thalassaemic women. Iron deficiency appears not to be a major health problem in this population. Haemoglobinopathies are common but, except for homozygous alpha(+)-thalassaemia, do not substantially contribute to anaemia in pregnancy. alpha(+)-Thalassaemia ameliorates malarial anaemia in pregnant women.