To determine the impact of a rapid and accurate rotavirus test in the emergency ward on the reduction of antibiotic prescription in children under 5 years old with acute diarrhea at "Arzobispo Loayza National Hospital", Lima, Peru. We performed an observational prospective randomized controlled study, from July 2008 to January 2009. Stool samples from patients with diarrhea lasting less than 5 days were analyzed. Out of 201 cases, 101 were classified in Group A (with fecal leukocytes test performed) and 100 in Group B (with fecal leukocytes test and rotavirus/adenovirus test performed). We aimed to associate the signs and symptoms with the decision of prescribing antibiotics and with hospitalization risk. Both groups were comparable with regard to age, weight and illness duration. In patients with rotavirus infection, fecal leukocytes were positive in 46.9% of cases. Frequency of antibiotic use was directly associated with the number of fecal leukocytes (P<0.0001). There was a higher risk of admission in the group positive to rotavirus than in the group negative to this agent (21.9% vs. 6.3, P<0.0001). No diarrhea-attributable deaths were reported. The use of rotavirus test in the pediatric emergency room decreased antibiotic prescription in children with diarrhea.