The objective of this paper was to study prospectively the course of clinically relevant thyroid dysfunction in a cohort of patients on long-term lithium treatment. Patients (N = 150) who had undergone a cross-sectional evaluation of their thyroid function in 1989, when they were at different stages of lithium treatment, were followed up for the presence of thyroid autoimmunity, hypothyroidism, and goiter during a further period of lithium exposure of up to ten years. The following annual rates of newly developed thyroid dysfunction were observed: autoimmunity (1.4%), subclinical hypothyroidism (1.7%), and goiter (2.1%). Subjects with thyroid autoimmunity had a higher chance of requiring substitution treatment with levothyroxine for subclinical hypothyroidism compared with subjects with no evidence of thyroid autoimmunity (13/32 = 41% versus 7/118 = 6%). Subjects (N = 15) who were prescribed carbamazepine in addition to lithium showed a significant decrease of TSH concentrations. In patients already being treated with lithium for several years, the overall incidence of hypothyroidism, goiter, and thyroid autoimmunity were comparable with those reported for the general population. However, lithium exposure may represent an additional risk factor for hypothyroidism in women and/or in the presence of thyroid autoimmunity.