Background Zonulin is a biomarker of impaired intestinal permeability, which has been associated with various disorders. The primary aim was to study serum zonulin (s-zonulin) in individuals with morbid obesity before and after a conservative weight loss intervention followed by bariatric surgery. The secondary aims were to explore predictors of s-zonulin, and the associations between the changes of the predictors and changes in s-zonulin, and to compare the associations in the two treatment periods. Methods Individuals with morbid obesity were included. Data before any weight loss interventions, after a 6 months' conservative weight loss intervention, and 6 months after bariatric surgery were used. S-zonulin was measured with an ELISA method from Immundiagnostik AB, Bensheim, Germany. Data were analysed with mixed models. Results The mean body mass index was 42.1 kg/m(2)(SD 3.8) at inclusion and was reduced to 38.7 kg/m(2)(SD 3.8) and 29.8 kg/m(2)(SD 3.8) after the conservative treatment and bariatric surgery respectively. S-zonulin was 63 ng/mL (SD 32) at inclusion and was reduced with 19 ng/ml (95% CI 12 to 26,p <0.001) after conservative treatment and 11 ng/ml (95% CI 0 to 21,p = 0.04) after bariatric surgery. At inclusion, s-zonulin was significantly associated with factors including p-glucose (B = 2.21, 95% CI 1.09 to 3.33,p <0.001), c-reactive protein (B = 1.02, 95% CI 0.45 to 1.58,p <0.001) and the intake of proteins (B = 0.23, 95% CI 0.08 to 0.38,p = 0.003) and non-nutritive sweeteners (B = 0.68, 95% CI 0.19 to 1.17,p = 0.007). The reduction in s-zonulin after the conservative weight loss intervention was significantly associated with improvement in diarrhoea (B = 6.6, 95% CI 1.3 to 11.8,p = 0.02), HbA1c (B = 9.7, 95% CI 1.1 to 18.3,p = 0.03), p-glucose (B = 3.5, 95% CI 1.2 to 5.9,p = 0.004) and gamma-GT (B = 0.28, 95% CI 0.09 to 0.47,p = 0.004), but not associated with the change in body mass index (B = 0.9, 95% CI - 1.5 to 3.3,p = 0.46). Conclusions S-zonulin was markedly reduced after the conservative weight loss intervention, and further reduced after bariatric surgery. The reduction in s-zonulin was associated with improvement of diarrhoea, markers of glucose intolerance and liver disease, but not associated with the change in body mass index.