Iron deficiency (ID) is the most common nutritional deficiency worldwide. Young children are at high risk of ID because of their rapid growth and consequent increase in iron requirement. Iron deficiency has variable and lasting adverse effects on children, most importantly on the growing brain, which includes behavioural deficits, impaired intellectual and motor dysfunctions. Many studies in children tend to focus more on iron deficiency anaemia (IDA). However, ID predates IDA and the deleterious effects of ID may be reversed with early identification and prompt intervention before anaemia develops. The current study therefore aimed to determine the prevalence of iron deficiency and the associated risk factors in apparently healthy children aged 4 months to 24 months at the Lagos University Teaching Hospital. The study was cross-sectional in design and conducted over five months. Four hundred and three apparently healthy children were recruited into the study from the well-baby clinic and immunization clinic at the Lagos University Teaching Hospital, Lagos. Information on sociodemographic characteristics, nutritional and medical history were obtained using a pre-tested questionnaire while anthropometric measurements on the children were recorded. Blood samples were collected from the participants and assayed for haemoglobin (Hb) level, serum ferritin (SF) and C-reactive protein (CRP). Serum ferritin and C-reactive protein were assayed using Enzyme Linked Immunosorbent Assay to detect subclinical infection. Iron deficiency was defined as SF less than 12µg/L if CRP was less than 5mg/L or SF less than 30µg/L if CRP was greater than or equal to 5mg/L. Haemoglobin level less than 11g/dL was documented as anaemia. Iron deficiency anaemia was defined as ID with anaemia.