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Background: Rotavirus infection is the single most common cause of acute gastroenteritis in children under five years of age. Rotavirus gastroenteritis has a high morbidity and mortality in children in Kenya. Objectives: To determine the short term clinical outcome for children admitted to Kenyatta National Hospital with rotavirus gastroenteritis and the correlates of poor outcome. Design: Short longitudinal survey. Setting: Kenyatta National Hospital from February to May 2008. Subjects: Five hundred children were screened using a rapid antigen detection kit and ELISA. Results: Of the 191 children who tested positive for rotavirus in stool; 172 children were recruited into the study. Eighty eight per cent of the patients were discharged within one week, 8.1% stayed for more than seven days while 4.1% died. Children who had co-morbidities such as malnutrition, rickets and pneumonia had worse outcomes. Conclusion: Rotavirus gastroenteritis has a long hospital stay and a high mortality. Children in shock on admission and those with co-morbid conditions should get priority for they have a poor outcome.