The incidence of Hashimoto's thyroiditis (HT) seems to have increased over the last several decades. Since there is a lack of recent studies in the literature that evaluate this phenomenon on a histological basis, we aimed to assess the incidence of lymphocytic thyroid infiltration (LTI) in our large surgical patient collective over a 31-year period. In our study, a total of 1,050 patients who had undergone uni- or bilateral thyroid surgery for benign goiter were included (150 patients in each group, during 1979 to 2009). The stored histological sections of the removed thyroid specimens were re-analyzed, including routine grading of LTI severity on a scale of 0-4, according to Williams and Doniach. Positive correlations were seen for the incidences of LTI grading (0-4) (r = 0.077, p = 0.013) and HT (r = 0.044, p = 0.078) over the years. Furthermore, when comparing the years 1979-1989 and 1994-2009, i.e., before and after the second iodine prophylaxis had been introduced in Austria, a higher incidence of HT was found for the later years (2 out of 450, 0.4%, vs. 6 out of 600, 1.0%, respectively; p < 0.0001). In conclusion, the data demonstrate that the incidence of LTI and HT has increased substantially over the last 31 years.