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Abstract Background The Democratic Republic of the Congo (DRC) is one of the countries with the highest rotavirus mortality rate in the world. The aim of this study was to describe the clinical features of rotavirus infection after the introduction of rotavirus vaccination of children in the city of Kisangani, DRC. Methods We conducted a cross-sectional study of acute diarrhoea in children under 5 years of age admitted to 4 hospitals in Kisangani, DRC. Rotavirus was detected in children’s stools by an immuno-chromatographic antigenic rapid diagnostic test. Results A total of 165 children under 5 years of age were included in the study. We obtained 59 cases of rotavirus infection, or 36% CI95 [27, 45]. The majority of children with rotavirus infection were unvaccinated (36 cases) and had watery diarrhoea (47 cases), of high frequency per day/per admission 9.6 ± 3.4 and accompanied by severe dehydration (30 cases). A statistically significant difference in mean Vesikari score was observed between unvaccinated and vaccinated children (12.7 vs 10.7 p-value 0.024). Conclusion Rotavirus infection in hospitalized children under 5 years of age is characterized by a severe clinical manifestation. Epidemiological surveillance is needed to identify risk factors associated with the infection.