The extent of thyroidectomy for well-differentiated thyroid cancer (WDTC) remains controversial. We compared outcomes of patients undergoing unilateral thyroid lobectomy (UTL) versus complete thyroidectomy (CT) to determine the best operative management of WDTC. We compared outcomes of patients who underwent UTL or CT for malignancy using the 1999 to 2003 editions of the National Inpatient Sample database. A total of 13,854 patients underwent UTL (n = 4,238) and CT (n = 9,616). The CT group was more likely to have complications than the UTL group (15% vs 6%, P < 0.0001). Mean total charges were higher in the CT group ($11,432) versus the UTL group ($9,739), as was LOS (2 days versus 1 day); P < 0.0001. Complete thyroidectomy is associated with increased morbidity, total charges, and length of stay. The higher risk of short-term complications should be considered when considering performing a complete thyroidectomy for WDTC.