BackgroundAntenatal iron supplementation is a cost effective way of reducing iron deficiency anaemia among pregnant women in resource limited countries like Uganda. Poor adherence to iron supplements has limited its effectiveness in reducing maternal anaemia as evidenced by the high burden of iron deficiency anemia in Sub-saharan Africa. The aim of this study was to determine the level of and factors associated with adherence to iron supplementation among women attending antenatal clinic at Mulago National Referral Hospital, Kampala, Uganda.MethodsThree hundred and seventy pregnant women were recruited in a cross sectional survey in Mulago National Referral Hospital antenatal clinic after informed consent between February and April 2014. Levels of adherence to iron supplements were assessed using visual analogue scale and factors associated collected using an interviewer administered questionnaire.ResultsAbout 12% (11.6%) of the mothers attending the antenatal clinic adhered to iron supplements over 30 day period. Mothers who had had four or more antenatal visits prior to the survey [odds ratio (OR) = 1.49, 95% confidence interval (CI) 1.12–1.97], had more than 2 week supply of iron supplements in the previous visit (OR 2.81, 95% CI 1.02–1.09), prior health education (OR 1.56, 95% CI 1.07–2.29) were more likely to adhere to iron supplements. Inadequate drug supplies and fear for side effects were the main reasons why participants missed the iron supplements.ConclusionsThere was low adherence to iron supplements among mothers attending antenatal clinic at Mulago National Referral Hospital. We recommend a national evaluation of adherence to iron supplements and look at ways of increasing adherence.