Background/Aims Glucose-6-phosphate dehydrogenase deficiency worsens the risk of anaemia and complicates gestation and birth if poorly managed. This study investigated the prevalence and factors associated with anaemia and this deficiency in pregnant women. Methods This cross-sectional study was conducted among 369 pregnant women at the Cape Coast Metropolitan Hospital, Ghana. Multiple logistic regression was used to investigate the relationship between anaemia and various sociodemographic variables. Results The prevalence of anaemia was 41.2% at 13 weeks' and 66.7% at 36 weeks' gestation. Overall, 29.8% of participants were glucose-6-phosphate dehydrogenase deficient. Age (P=0.024)and marital status (P=0.009) were significantly associated with anaemia at 13 weeks. Gravidity (P=0.014) and employment status (P=0.001) were significantly associated with anaemia at 36 weeks. Conclusions There was a high prevalence of co-morbid anaemia and glucose-6-phosphate dehydrogenase deficiency at 13 and 36 weeks' gestation. Future studies should consider genetic and dietary factors that may contribute to gestational anaemia. Implications for practice Clinicians and midwives should be aware of the factors that can affect anaemia and glucose-6-phosphate dehydrogenase deficiency, particularly in areas where deficiency is prevalent. Early detection could allow individualised treatment.