A hundred and eighty‐six students were randomly selected from Federal Government Secondary Schools and Lagos State Secondary Schools. Stool specimen were collected for intestinal parasites investigation. Haematological and serological screening including haemoglobin concentration estimation were carried out and information were collected on their school meals. The study showed that 45.2% did not eat school meals of which 60% were anaemic while 40% were not. Investigation showed 20% in the Lagos State Secondary Schools did not usually eat school meals, 62.5% were anaemic while 37.5% were not. There were no significant association between haemoglobin level and intake of school meals in both Federal Government Secondary and Lagos State Secondary Schools. Fifty‐six (85%) of those who took school meals were iron deficient. Similar investigation shows that ninety‐four (98%) of the Lagos Secondary School students who took school meals were iron deficient. Chi‐square test in the comparative study showed a significant association between MCHC and the type of school meals take (p <50).Pearson correlation p<.05 coefficient showed a significant association between haemoglobin level and the ethnic group.