Objective: To analyze the etiology of intestinal pathogens in children hospitalised at the Department of Pediatric Infectious Diseases, University Hospital, Brno, in 2015-2016 with a focus on rotavirus gastroenteritis (RVGE). Methods: A retrospective study evaluates pediatric patients aged 0-18 with symptoms of gastroenteritis hospitalized from January 1, 2015 to December 31, 2016. Rectal swabs for cultivation of the intestinal pathogens were collected from all patients and, in some cases, the stool samples for the identification of viral antigens and for the detection of Clostridium difficile. Results: Patients with gastroenteritis were hospitalized in a total of 1083 in 2015 and 988 in 2016. We proved a viral infection at 36.0% and 29,0% in 2015 and 2016, respectively. RVGE were confirmed in 28.2% and 18.2%, adenovirus gastroenteritis in 3.2% and 5.0%, norovirus gastroenteritis in 4.6% and 5.8%. Both years bacterial infections were confirmed in 14.6% of patients, most of them salmonellosis (9.3%, 8.3%), less campylobacteriosis (4.2%, 5.2%), the clostridial colitis (0.9%, 0.7%) and the least of all yersinioses (0.0%, 0.4%). No one was hospitalized with an infection caused by Shigella spp. Etiology remained unclear in 49.7% and 56.6% cases in 2015 and 2016, respectively. Maximum cases of viral diseases occurred in children under 5 years of age (83.3%, 82.5%), specifically in the age group 13-36 months (44.6%, 47.6%). The highest number of cases in patients with RVGE were also in children under 5 years of age (82.3%, 80.6%) and 13-36 months (41.0%, 42.8%). Maximum cases of bacterial diseases occured in children over 5 years of age (54.4%, 46.5%). Most RVGE were registered in April 2015 and in March and April 2016. Conclusion: Patients with RVGE, even at a time of available vaccination, form a significant proportion of patients treated for gastroenteritis (23.4%).