BACKGROUND Our objective was to analyse trends in thyroid surgery in Wales over a recent 12-year period. METHODS Details of patients who underwent thyroid surgery across Wales from 1999 to 2010 were analysed from the Patient Episodes Database for Wales [n = 6570, 83% (5429) female, 86% (5634) benign thyroid disease]. We determined age-adjusted thyroidectomy rates from the European standard population and a Poisson regression model was fitted to assess temporal trends. Joinpoint regression was used to calculate annual percentage change (APC) in thyroidectomy rates. RESULTS An increase in thyroidectomy rates was observed for malignant disease [APC 4.5, 95% confidence interval (CI) 1.6-7.5] while surgery rates for benign disease declined over the period (APC -3.2, 95% CI -5.1 to -1.3). The use of total thyroidectomy rose from 17% (599/3501) in 1999-2004 to 30% (912/3069) in 2005-2010 (p < 0.001). Total thyroidectomies were performed in a higher proportion of males than females [26% (291/1141) vs. 22% (1220/5429), p = 0.03] and in a greater percentage of patients with malignant disease than benign [36% (337/936) vs. 21% (1174/5634), p < 0.001). General surgeons undertook 83% of thyroid surgery but with a growing involvement of ENT surgeons. Regional disparities were seen in the type of surgery offered to patients with benign thyroid disease. CONCLUSIONS The use of total thyroidectomy for benign and malignant thyroid disease has risen in Wales. The increase in surgeries performed for malignancy would support a rising incidence of thyroid cancer in the region. Regional disparities in choice of surgery for benign disease require further exploration.