Anaemia still persists among children and women of childbearing age in Palestine. We investigated the prevalence of anaemia and associated factors among Palestinian school adolescents (aged 13–15 years) in Ramallah and Hebron governorates. Haemoglobin levels were measured to assess the prevalence of anaemia. The prevalence of anaemia was significantly higher in Hebron than in Ramallah among boys (22.5% versus 6.0% respectively), while among girls the figures were similar (9.2% and 9.3% respectively). Linear binomial regression analysis showed that among boys, anaemia was independently associated with residence in Hebron and higher standard of living, while among girls, anaemia was associated with higher father’s education. Consumption of iron-rich foods, as recorded in food frequency questionnaires, had no significant effects on anaemia prevalence in both boys and girls.