Background <p>Congenital duodenal obstruction (DO) is an anomaly which requires surgery shortly after birth. However, its long-term gastrointestinal (GI) sequelae remain unknown. Therefore, this study aimed to determine the long-term GI patient-reported outcome measurements (PROMs) using the Pediatric Quality of Life Inventory™ (PedsQL™) GI-Module in patients with DO compared to healthy controls. Secondly, we evaluated the PROMs comparing patients with DO with and without trisomy 21.</p> Methods <p>We performed a cross-sectional cohort study (September-December 2023). The PedsQL™ GI-Module questionnaire was sent to all patients who underwent DO surgery between 1999 and 2022. Data were compared with a published healthy control group (<i>n</i> = 513). Bonferroni correction was used to adjust for multiple tests.</p> Results <p>In total, 33/89 patients completed the PedsQL™ GI-Module questionnaire. The majority of the patients were female (<i>N</i> = 19/33) with a mean age of 13.3 years (SD ± 6.6). Trisomy 21 was diagnosed in seven patients. The DO group had a similar mean total score compared to healthy controls (84.5 ± 11.5 vs. 88.6 ± 12.9,<i>p</i> = 0.075). The mean score for constipation (77.2 ± 22.0 vs. 86.9 ± 17.6,<i>p</i> = 0.002) was significantly lower compared to the healthy controls, indicating a worse outcome, whilst all other domains were similar. Four patients used laxatives. Patients with DO and trisomy 21 had similar scores compared to patients with DO without trisomy 21.</p> Conclusion <p>The results showed similar long-term GI PROMs in patients who underwent DO surgery compared to healthy controls. Patients with DO experienced constipation more frequently, emphasizing the need for attention during follow-up and education of (parents) of patients. Additionally, children with DO and trisomy 21 showed similar PROMs to those without trisomy 21.</p> Level of evidence <p>II.</p>