Thyroid surgery is considered a clean procedure, and therefore antibiotic prophylaxis is not recommended. However, antibiotic prophylaxis is often used in clinical practice. Aim of the present study is to show the rate of infections in thyroid surgery and whether antibiotic prophylaxis, among other factors, is associated with a lower infection rate in 2,926 patients (constituting the cohort of UEC-Italian Endocrine Surgery Units Association) who had a thyroid surgical operation between the years 2009 and 2011. Antibiotic prophylaxis was used in 1,132 interventions (38.7 %). We recorded 28 cases of infections (rate = 1 %). At univariate analysis the lack of drainage and of antibiotic prophylaxis were factors associated with infection development. However, we noticed a concentration of cases of infections (10 of the 28 total cases) in one single center that showed a very high rate of infection (8.8 %). At logistic regression analysis the only independent predictor of infection development was belonging to that center, while the lack of antibiotic prophylaxis was not. In conclusion, our study shows that infection rate in thyroid surgery was 1 %. The use of an antibiotic prophylaxis was not associated with a protection from these infections.