This study aimed to characterise the clinical condition of Gambian children presenting with persistent diarrhoea and severe protein energy malnutrition and to evaluate the effects of short term in-patient treatment in terms of long-term outcome. Twenty-two children (aged 6 to 36 months) with persistent diarrhoea (greater than or equal to four loose stools/day for more than two weeks) and severe malnutrition (weight-for-height less than 75% of the National Center for Health Statistics median value) were assessed prior to in-patient treatment for three weeks with antibiotics and high nutrient-density milk. Initial assessment included biochemical and immunological status together with stool microbiology. Criteria for discharge--cessation of diarrhoea for five consecutive days and steady weight gain--were met in all subjects within four weeks. Progress was assessed clinically and anthropometrically at weekly intervals and 6 and 12 months following discharge. Results showed a steady improvement in growth during the period of in-patient treatment. Continuing improvement in weight-for-age and mid-upper arm circumference was observed after 6 and 12 months and weight-for-height continued to improve up to 6 months but fell back by 12 months. This study has demonstrated that, in the treatment of persistent diarrhoea in the tropics, relatively short periods of in-patient rehabilitation, whilst leading to a resolution of diarrhoeal symptoms and weight gain in the short term, do not lead to complete recovery. Persistent diarrhoea and malnutrition are likely to recur when the child returns to his village.(ABSTRACT TRUNCATED AT 250 WORDS)