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Background: Vitamin D (25(OH) D3) levels in pouch patients are not well defined.Aim: To evaluate the frequency and factors associated with low 25(OH) D3 levels in pouch patients with underlying inflammatory bowel disease (IBD).Methods: A consecutive of 157 pouch patients was identified from our Pouchitis Registry. A sample of 155 ulcerative colitis (UC) patients without IPAA served as controls.Results: The mean age of the cohort was 37.5 ± 14.2 years, with 86 (54.8%) being female. Low 25(OH)D3 levels (< 31 ng/mL) were detected in 69.4% of patients (N = 109). 34 (21.7%) of the 157 patients examined were 25(OH)D3 deficient (< 20 ng/mL). This was higher than the frequency of vitamin D insufficiency or deficiency in a sample of UC patients without IPAA. Between patients with and without normal 25(OH) D3 levels (> 31 ng/mL), no differences were identified in terms of demographic, pouch, and medication variables. A low hemoglobin level was found to be associated with low 25(OH) D3 levels in both univariate (p = 0.02) and multivariate analyses (odds ratio [OR] = 3.37; 95% confidence interval [CI]: 1.41–8.06; p = 0.01). Low levels of 25(OH)D3 was not related to markers of pouch inflammation, in particular there was no relation to pouchitis (OR = 1.20; 95% CI: 0.41–3.52; p = 0.74).Conclusion: Low 25(OH)D3 level was common in this cohort, irrespective of inflammation of the pouch, possibly suggesting a strategy of routine testing in this population. Anemia was found to be associated with a low 25(OH)D3 level.