BackgroundAnaemia is one of the major causes of death among children under five years in Africa, with a prevalence of 64.6% among pre-school children. In 2014, we conducted a cross-sectional study in Namutumba district in East-central Uganda to determine the prevalence and factors associated with anaemia among children aged 6 to 59 months.MethodsWe conducted a household survey in 376 randomly selected households. One child aged 6 to 59 months was randomly sampled from each selected household. A structured questionnaire administered to an adult caregiver was used to collect household data. Blood was collected by finger or heel prick to estimate the haemoglobin level using a portable haemocue analyser. Anthropometric data including age, weight and height was collected for each child. A modified poisson regression model was used to determine the correlates of anaemia, prevalence ratios and their 95% confidence intervals (CI).ResultsThe prevalence of anaemia was high (58.8%) and was highest among children aged 12 to 23 months (68.5%) and males (61.3%). About 27.7% children were stunted. Children aged 6–11 and 12–23 months were more likely to be anaemic (APR = 1.12; 95% CI: 1.05–1.19 and APR = 1.12; 95% CI: 1.00–1.24 respectively), Resident of Magada and Namutumba (urban areas) were less likely to be anaemic (APR = 0.89; 95% CI: 0.87–0.91and APR = 0.86; 95% CI: 0. 85–0.88 respectively). Children of caretakers of a big family size (seven or more children) and with any formal education were less likely to be anaemic (APR = 0.94; 95% CI: 0.89–0.99 and APR = 0.93; 95% CI: 0.87–0.99). Stunting (HAZ scores) was a predictor of anaemia (APR = 1.07; 95% CI: 1.02–1.12).ConclusionAnaemia is highly prevalent among children and there is need to invest in measures to prevent anaemia, especially among children in the rural areas.