BACKGROUND Inflammatory bowel disease (IBD) is a chronic gastrointestinal disease that is separated into two types: ulcerative colitis (UC) and Crohn's disease (CD). Although dysphagia is a well-studied and important topic in head and neck cancers and neurological disorders, research on the relationship between IBD and swallowing problems is not yet elucidated. The aim of this study was to compare swallowing function in the UC and CD using objective and patient-reported evaluation modalities. METHODS This was a prospective cross-sectional research with 86 patients (50 UC and 36 CD) treated at the gastroenterology department. The assessment includes flexible fiberoptic endoscopic examination (FEES). The penetration-aspiration scale, the functional oral intake scale (FOIS), the functional outcome swallowing scale (FOSS), the Eating Assessment Tool-10 (EAT-10) test, the Yale Pharyngeal Residue Severity Scale for vallecula (Yale PRSS-vallecula) and pyriform sinus (Yale PRSS-PS) were all used to determine extent of dysphagia. RESULTS The CD group had higher EAT-10 scores than UC group (p = 0.014). In terms of PAS scores, there was no significant difference between the two groups in all three food types (water, yogurt, and crackers) (p > 0.05). There was not a statistically significant variance between the groups in terms of vallecular residue (p > 0.05) according to the Yale PRSS-vallecula. Based on the Yale PRSS-PS, the CD group had significantly more residue than the UC group with yogurt and cracker (p = 0.014 and 0.030, respectively). FOSS and FOIS scores did not vary significantly between the two groups (p > 0.05). CONCLUSIONS CD impairs subjective and pharyngeal swallowing functions more than UC. It is obvious that swallowing should be assessed in patients with IBD.