Objectives: To assess the prevalence of prolonged and persistent diarrhoea, to estimate their co-occurrence with acute malnutrition and association with demographic and clinical factors.

Methods: Case-control study where cases were children under 5 years of age with diarrhoea and controls were children without diarrhoea, frequency-matched weekly by age and district of residency. Controls for cases 0-11 months were recruited from vaccination rooms and controls for cases 12-59 months were recruited by house visits using random locations in the catchment area of the study sites. Data were analysed by mixed model logistic regression.

Results: We enrolled 1134 cases and 946 controls. Among the cases, 967 (85%) had acute diarrhoea (AD), 129 (11%) had ProD and 36 (3.2%) had PD. More cases had acute malnutrition at enrolment (17% vs 4%, p<0.0001) and more were born prematurely (5.7% vs 1.8%, p<0.0001) than controls. 75% of ProPD cases did not have acute malnutrition. Cases with AD and ProPD had different symptomatology, even beyond illness duration.

Conclusions: ProPD is common among children presenting with diarrhoea and is not confined to children with acute malnutrition. There is an urgent need for studies assessing causes of ProPD with and without acute malnutrition to develop treatment guidelines for these conditions.