Bariatric surgery is a widely used procedure for the treatment of obesity. Our aim is to describe the main immunological changes in patients who undergo bariatric surgery.A prospective study was conducted within a cohort of patients undergoing bariatric surgery and without previous evidence of systemic or organ-specific autoimmune diseases in whom 3 blood samples were collected - one day before surgery (Time 0), and 5 (Time 1) and 10 months (Time 2) after surgery.Thirty four obese patients underwent surgery (Time 0):30(88.24%) were women, mean age 38.3 years. When comparing Time 0 and Time 2, there were statistically significant changes in CD4+T cell count, with an increase from 1074/mL(IQR:860-1316) to 1217.5/mL(IQR:838-1510),p = 0.0002. The CD4/CD8 ratio increased from 2.2(IQR: 1.7-2.7) to 2.4(1.8-2.8), p = 0.0001. As for humoral variables, the C3 fraction of complement decreased from 164 ± 40.6 mg/dL to 112.4 ± 31.4 mg/dL(p < 0.001) and C4 decreased from 29.3 ± 10.1 mg/dL to 22.5 ± 7.1(p = 0.0009) at Time 2. Four patients with negative ANAs at baseline, showed positive ANAs at Time 2.One patient developed anti-citrullinated peptide antibodies >200 IU/mL at Time 2.Patients undergoing bariatric surgery show immunological changes which might eventually lead to develop an autoimmune disease.