Objectives: The aim was to show the most common indications for gastroscopy and colonoscopy in children, the dependence of indications for gastroscopy and colonoscopy on the age and sex of children and the frequency of overlapping indications for gastroscopies and colonoscopies and pathohistological findings, at the Department for Pediatrics, University Hospital of Split. Subjects and methods: The study included a total of 822 patients who underwent gastroscopy and colonoscopy at the Department of Pediatrics, University Hospital of Split in the period from 1 January 2016 to 31 December 2020. The data were collected from the protocol on gastroscopy and colonoscopy of the Department for Pediatrics, University Hospital of Split and the electronic database of the Department for Pathology, Forensic Medicine and Cytology, University Hospital of Split. The following data are included in the database: gender of the subjects, date of birth, date of the examination, indications and pathohistological findings. There were a total of 690 subjects on gastroscopy and 132 subjects on colonoscopy. Results: Among the subjects who underwent gastroscopy, the most common indication was malabsorption syndrome (N = 110; 15.94%), the next most common indication was abdominal pain (N = 103; 14.93%), followed by gastritis (N = 79; 11.45%) and celiac disease (N = 75; 10.85%). The most common indication for colonoscopy are inflammatory bowel disease, the most common indication is Crohn's disease (N = 33; 25%), followed by suspected inflammatory bowel disease in general (N = 24, 18.18%), and ulcerative colitis (N = 18; 13.64%). In patients who underwent colonoscopy overlapping between indications and pathohistological findings was 1.43 times more frequent than in patients who were found on gastroscopy. Conclusions: This study represents the most common indications for gastroscopy and colonoscopy in children, the influence of age and gender on the indications, and the frequency of overlapping between the indications and pathohistological findings. The results are comparable with similar research from the world literature.