Introduction: Rotavirus infection is the most common cause of acute diarrhoea in all European countries. In contrast, norovirus aetiology is becoming more common in countries where rotavirus vaccination has become a standard practice. Aim: The aim of the paper was to assess the aetiology and the clinical course of acute gastroenteritis in children hospitalised in the Department of Paediatrics, Paediatric Nephrology and Allergology of the Military Institute of Medicine. Materials and methods: Medical records of children hospitalised in the Department of Paediatrics, Paediatric Nephrology and Allergology of the Military Institute of Medicine in Warsaw between January and December 2018 due to gastroenteritis were analysed retrospectively. The study group included children diagnosed with acute gastroenteritis who had microbiological stool analysis performed. Results: Gastroenteritis of unknown aetiology was diagnosed in 93/155 children, rotaviral aetiology in 37, adenoviral aetiology in 7, and noroviral aetiology in 5 children. Stool culture was positive for Salmonella spp. in 5 children. Furthermore, mixed aetiology was found in 8 children (rotavirus/adenovirus in 5, and rotavirus/norovirus in 3 children). Rotaviruses were the most common aetiology of gastroenteritis among children aged ≤2 years. Vomiting and diarrhoea were the only symptoms in 48 and 40 children, respectively. The symptoms co-occurred in 67 children. Increased C-reactive protein (CRP) was found in patients with adenoviral aetiology and Salmonella spp. infection. We observed statistically more common low CRP levels and increased aminotransferase levels in patient with rotavirus infection. Conclusions: Rotaviruses were the most common aetiology of acute gastroenteritis in the study group. The clinical picture of rotavirus infection is dominated by vomiting and diarrhoea, which are relatively often accompanied by transient hypertransaminasemia.