Stress induces autoimmune disorders by affecting the immune response modulation. Recent studies have shown that shift work stress may enhance the onset of the autoimmune Graves hyperthyroidism. On the other hand, the possible association between occupational stress and autoimmune hypothyroidism has not yet been investigated. In order to detect the possible association between shift work and subclinical autoimmune hypothyroidism we investigated the prevalence of isolated anti-peroxidase thyroid (TPO) autoantibodies in 220 shift workers and in 422 day-time workers. Subclinical autoimmune hypothyroidism was diagnosed by the concomitant presence of high anti-TPO values and TSH levels higher than 2.51 mU/l. Anti TPO antibodies were measured by chemiluminescent technology (Advia Centaur) (a value above 60 IU/l was considered altered). Subclinical autoimmune hypothyroidism was diagnosed in 7.7 percent shift workers and in 3.8 percent day-time workers with a statistically significant difference: Odds Ratio (OR) 2.12, 95 percent Confidence Interval (CI) 1.05 to 4.29; p=0.03. The difference persisted after multivariate analysis taking into account age, sex, smoking habits, alcohol intake, familial history of autoimmune thyroid disease and exposure to radiation as possible confounders: OR. 2.24, 95 percent CI.1.01 to 4.94, p 0.05. Altered anti- TPO autoantibodies were found in 13.6 percent shift workers and in 8.6 percent day-time workers OR. 1.64, 95 percent CI.1.03 to 2.74, p=0.05. The significant difference was still detectable after multivariate analysis: OR. 1.95, 95 percent CI. 1.09 to 3.48, p=0.02. Our data show a significant association between shift work and autoimmune hypothyroidism. This finding may have implications in the health surveillance programs.