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Background  Early childhood is an age at risk of anaemia and its deleterious consequences. In Sudan, there is limited evidence on the prevalence and determinant of anaemia in under-five children. This study was conducted in Sudan to assess the prevalence of anaemia in children and to identify its determinants.    Methods  We conducted a household survey involving children aged 6 months to 5 years in November 2016. A representative population was sampled across rural, urban and camps settlements across 18 states in Sudan. We used a pre-designed questionnaire data collection. Haemoglobin (Hb) level and malaria infection were checked. In this cross-sectional study, we dichotomized the outcome variable and performed logistic regression analyses.    Results  A total of 3094 children under 5 years enrolled in the study, 1566 (50.6%) of them were female and 690 (22.3%) of them were under 2 years old. Anaemia prevalence in the whole cohort (6 months - < 5 years) was 49.4% and the mean haemoglobin concentration was 108.1 (standard deviation (SD): 15.4) g/L. The prevalence in younger (6 months - < 2 years) children (61.9%) was higher than in older (2 - < 5 years) children (45.6%) ( p  < 0.001). Severe anaemia (Hb < 70 g/L) prevalence in the whole population was 1.6%. Age (Odds ratio (OR) 2.25, 95% confidence interval (95%CI) 1.75–2.90,  p  < 0.001), type of place of residence (OR 0.37, 95%CI 0.18–0.74,  p  = 0.005), maternal anaemia (OR 1.74, 95%CI 1.39–2.17,  p  < 0.001), and malaria infection (OR 2.82, 95%CI 1.56–5.11,  p  < 0.001) were the identified predictors of anaemia in the whole cohort. In younger children, only the economic class was an anaemia predictor, with a lower anaemia risk among the rich wealth class (OR 2.70, 95%CI 1.29–5.62,  p  = 0.008). However, in older children, three anaemia predictors were identified. These are maternal anaemia (OR 1.79, 95%CI 1.40–2.28, < 0.001), malaria infection (OR 2.77, 95%CI 1.48–5.21,  p  = 0.002), and type of residency (where camps’ residents were less likely affected with anaemia than rural children (OR 0.38, 95%CI 0.17–0.87,  p  = 0.022)).    Conclusions  About half of the under-5 children in Sudan are anaemic, with worse prevalence in younger children. Efforts targeted at improving socio-economic status, decreasing maternal anaemia and childhood malaria infection may mitigate this alarming trend.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12887-020-02434-w.

Anaemia prevalence and determinants in under 5 years children: findings of a cross-sectional population-based study in Sudan