This study estimated the prevalence of anaemia and associated factors in a probability sample of 993 children aged 6-59 months in Cape Verde, West Africa. Odds ratio (OR) and 95% confidence interval (95% CI) were estimated from a hierarchical model for multiple analysis to assess the association between anaemia and explanatory variables. The prevalence of anaemia was 51.8% (95% CI 47.7-55.8). Children who resided within poor household conditions (OR 1.99; 95% CI 1.06-3.71) were below 24 months of age (OR 3.23; 95% CI 2.03-5.15) and recently experienced diarrhoea (OR 1.58; 95% CI 0.99-2.50) were at high risk of anaemia. Anaemia should be considered a serious public-health concern in Cape Verde, mainly for children below 24 months. Further, special consideration should be given to children who have experienced recent diarrhoea and belong to families residing in poor household conditions.