Introduction The function of an ileal pouch–anal anastomosis (IPAA) has high impact on the patients’ quality of life (QoL), and, hence, objective methods for examination of the function are warranted for a better understanding of the functional result and possible treatment of dysfunction. Studies on defecography and pouch function have shown ambiguous results. Intestinal transit time could theoretically affect pouch function but reports in patients with an IPAA are rare. The objective of this study was to evaluate scintigraphic intestinal transit time, scintigraphic defecography and any association with QoL and pouch function. Method It is a cross-sectional study including 20 patients with ulcerative colitis and an IPAA. Scintigraphic transit time was determined after oral administration of a Tc-99m-labelled omelette. Defecography was performed with instillation of a radioactive labelled paste. Ejection fraction (EF) was measured after defecation and one hour later. QoL was estimated by the Short Inflammatory Bowel Disease Questionnaire (SIBDQ). Pouch function in terms of bowel movements, pouch volume, and incontinence were self-reported on a separate questionnaire. Pouchitis was evaluated by endoscopy and pouch biopsy. Results We included 9 men and 12 women with a median age of 41 yrs [26-68]. Median BMI was 24 [19-36] and follow-up was 932 days [481-3491]. A median daily stool frequency of 8.5 [4-25] was reported and 3 (15%) patients suffered from incontinence. No patients had symptomatic or endoscopic pouchitis; however, the histology showed inflammation in 15 (71%) patients. Median pouch volume was 222 mL [100-360] and SIBDQ score 55 [22-67]. Median transit time was 180 min [80-365]. Median EF at first defecation was 49% [8-75] and 66% [27-97] at the second. We found a slower transit time in patients with high BMI (p = 0.006), but no correlation between transit time and pouch function. We found no association with EF. Conclusion Intestinal transit time and defecography are feasible methods in patients with IPAA, and allows estimation of pouch volume and EF. In this small series, intestinal transit time was associated to BMI, but there was no association between clinical symptoms and objective measurements of pouch function.