Abstract Background Patients with ulcerative colitis (UC) undergoing total proctocolectomy with ileal pouch anal anastomosis (pouch surgery) may be prone to develop nutritional deficiencies. Here we aimed to evaluate the rates of vitamin deficiencies and their risk factors in these patients. Methods Patients after pouch surgery were consecutively enrolled in a tertiary referral center. Pouch behavior determined clinically (normal pouch; recurrent acute pouchitis; chronic pouchitis; Crohn’s like disease of the pouch), disease activity, inflammatory markers and serum vitamin D, B12 and folic acid levels were repeatedly assessed. Body mass index (BMI) and the use of dietary supplements were recorded at each visit. Results A total of, 136 patients (mean age-, 47.5±16 years, mean BMI-, 24.9±5 Kg/m2, female gender, 58%) underwent, 721 study visits. Average visits/patients:, 5 (range, 1–15); between-visit interval:, 5±4 months. Normal pouch:, 41%, recurrent acute pouchitis, 24%, chronic pouchitis/ Crohn’s like disease of the pouch:, 35%. Vitamin D deficiency (<25 nmol/L) and insufficiency (25–75 nmol/L) were detected in, 6.5% and, 82% of patients, respectively. Vitamin B12 deficiency (<221 pmol/L) was detected in, 29%, and folic acid deficiency (<7 nmol/L) in, 9.5% of patients. After controlling for disease activity and inflammatory markers, vitamin D deficiency was positively associated with pouch age (i.e interval from the ileostomy closure, OR=, 1.47, 95%CI, 1.1–1.9, p=, 0.007). Vitamin B12 deficiency was positively associated with BMI (OR=1.07, 95%CI, 1.001–1.14, p=0.045), and folic acid deficiency was inversely associated with patient’s age (OR=, 0.95, 95%CI, 0.9–0.99, p=0.017). Of patients with vitamin D, B12 and folic acid insufficiencies or deficiencies, only, 60/121 (49.6%), 17/40 (42%), and, 4/13 (30%), respectively, reported the use of appropriate dietary supplements throughout the long-term follow-up. Conclusion In a longitudinal follow up of patients with UC after pouch surgery, we detected significant vitamin D, B12 and folic acid deficiencies and identified specific risk factors. Insufficient active correction with dietary supplements was noticed. Screening and improved correction of nutritional deficiencies should be a part of the routine pro-active multidisciplinary care of patients after pouch surgery.