Abstract This study aimed to critically review pediatric swallowing assessment data to determine the future need for standardized procedures. A retrospective analysis of 152 swallowing examinations in 128 children aged 21 days to 18 years was performed. The children were presented at a university dysphagia center between January 2015 and June 2020 for flexible-endoscopic evaluation of swallowing (FEES). Descriptive analysis was conducted for the sample, swallowing pathologies, diagnosis, and missing values. Using binary logistic regression, the relationship between dysphagia and underlying diseases was investigated. The largest group with a common diagnosis in the cohort were children with genetic syndromes (n = 43). Sixty-nine children were diagnosed with dysphagia and 59 without dysphagia. The non-dysphagic group included 15 patients with a behavioral feeding disorder. The presence of an underlying disease significantly increased the chance of a swallowing problem (OR 13.08, 95% CI 3.66 to 46.65, p = .00). In particular, the categories genetic syndrome (OR 2.60, 95% CI 1.15 to 5.88) and neurologic disorder (OR 4.23, 95% CI 1.31 to 13.69) were associated with higher odds for dysphagia. All pediatric FEES were performed without complications, with a completion rate of 96.7%, and with a broad variability of implementation. Several charts lacked information concerning swallowing pathologies, though. Generally, a more standardized protocol and documentation for pediatric FEES is needed to enable better comparability of studies on epidemiology, assessment, and treatment outcomes in future.