In endemic areas iodine deficiency, and in iodine sufficient regions autoimmune thyroiditis, is the first aetiological factor for goitre. The aims of this study were to determine the incidence of iodine deficiency and autoimmune thyroiditis in patients presenting with goitre, to compare clinical and ultrasonographic assessment of thyroid size and to investigate the relationship between iodine and autoimmune thyroiditis. Patients diagnosed with goitre clinically (n = 204) were evaluated by their anthropometric measurements, ultrasonographic examination of the thyroid gland, thyroid function and TRH stimulation tests, thyroid autoantibodies and morning urinary iodine measurements. Thyroid volumes were evaluated according to three different reference criteria. Incidences of iodine deficiency and autoimmune thyroiditis were 54% and 17%. The incidences of iodine deficiency and excess were not significantly different in the autoimmune group (n = 35) compared to the non-autoimmune group (n = 169). In the autoimmune group, urinary iodine concentration correlated positively with serum thyroid hormones (FT3 r = 0.42, TT3 r = 0.38, TT4 r = 0.34) and negatively with serum TSH levels (r = 0.45). There were discrepancies between clinical and ultrasonographic evaluation of goitre, and between different reference criteria. This study revealed that iodine deficiency is still the first aetiological factor for goitre in our region and failed to show a relationship between iodine intake and autoimmune thyroid disease.