Anaemia due to iron deficiency is still a widespread problem. Among adolescent girls, it will bring negative consequences on growth, school performance, morbidity and reproductive performance. This cross sectional study aimed to identify the different nutritional and iron status characteristics of young adolescent girls 10-12 years old with iron deficiency anaemia and anaemia without iron deficiency in the rural coastal area of Indonesia. Anaemic girls (N =133) were recruited out of 1358 girls from 34 elementary schools. Haemoglobin, serum ferritin, serum transferrin receptor and zinc protophorphyrin were determined for iron status, whilst weight and height were measured for their nutritional status. General characteristics and dietary intake were assessed through interview. Out of 133 anaemic subjects, 29 (21.8%) suffered from iron deficiency anaemia, which was not significantly related to age and menarche. About 50% were underweight and stunted indicating the presence of acute and chronic malnutrition. The proportion of thinness was significantly higher (P < 0.05) among subjects who suffered from iron deficiency anaemia (51.7% vs. 29.8%). Furthermore, thin subjects had a 5 fold higher risk of suffering from iron deficiency anaemia (P< 0.05) than non-thin subjects (OR: 5.1; 95%CI 1.34-19.00). Further study was recommended to explore other factors associated with anaemia and iron deficiency anaemia, such as the thalassemia trait and vitamin A deficiency. The current iron-folate supplementation program for pregnant women should be expanded to adolescent girls.