Iron deficiency anaemia has been described as the commonest nutritional deficiency in infancy and childhood. It is a recognized public health problem in children that adversely impacts childhood morbidity and mortality and impairs cognitive and behavioural development. In Sagamu, information on the prevalence and risk factors of iron deficiency anaemia is limited. This study sought to investigate prevalence and risk factors of iron deficiency anaemia in children aged 1 year to 5 years at the Olabisi Onabanjo University Teaching Hospital, Sagamu, Ogun State. This cross - sectional study was carried out over a six-month period, between October 2014 and March 2015 at the Children's Out-patient clinic of the Olabisi Onabanjo University Teaching Hospital (OOUTH) involving 422 children between 1 and 5 years of age. Serum iron, serum ferritin, total iron binding capacity and transferrin saturation were assayed in the subjects. Identification of parasites from freshly passed stool samples was also done. The primary outcome measured was iron deficiency anaemia, defined as haemoglobin values less than the WHO threshold, <11.0g/dl, with the presence of two or more of the following parameters; mean corpuscular volume (MCV) < 70 fl, serum ferritin < 12ng/dl, and transferrin saturation < 16%. Data was processed using SPSS version 23.0 and analysis included Fishers Exact test to determine association between variables, Student’s t test to compare means and logistic regression analysis.