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Background: In patients with sickle cell anaemia (SCA), recurrent episodes of sequestration, micro-infarction, ischaemia and necrosis within the renal cortex cause nephron damage. Micro-albuminuria results from compensatory mechanisms aimed at preserving the glomerular filtration rate. Aims: To establish the prevalence of micro-albuminuria among children with SCA and to describe associated factors. Methods: A cross-sectional study of patients aged 2-18 years with SCA was undertaken at the sickle cell clinic, Mulago Hospital, Kampala between November 2007 and April 2008. Haemoglobin was measured and urine dipstick was used to determine protein, glucose, red blood cells and nitrites, serum creatinine and albumin and urine creatinine and albumin. Binary logistic regression was performed to determine factors associated with micro-albuminuria. Results: Of 305 children studied, 48·2% were male. The mean (SD) age of the study participants was 9·7 (4·9) years. The prevalence of micro-albuminuria (30-300 μg/mg) was 28·2% (86/305, 95% CI 23·1-33·3). Use of diclofenac (p = 0·01) and ibuprofen (p = 0·001) were found to increase the risk of micro-albuminuria only by bivariate analysis. By multivariate analysis, increasing age (p = 0·001), a higher number of blood transfusions (p = 0·001) and presence of urine nitrites (p = 0·031) were associated with a risk of micro-albuminuria, whereas high levels of haemoglobin (p = 0·018) were protective. There was no association between estimated glomerular filtration rate and micro-albuminuria. Conclusions: The prevalence of micro-albuminuria among children with SCA is relatively high. SCA patients over 5 years of age should be screened for micro-albuminuria. Those with lower haemoglobin levels should be monitored closely because of its association with micro-albuminuria. [ABSTRACT FROM AUTHOR]