Purpose Hashimoto's thyroiditis is an autoimmune disease affecting the thyroid, which may or may not be accompanied by hypothyroidism. Systemic lupus erythematosus (SLE) is a systemic autoimmune disease affecting all organ systems. The aim was to present a cohort of lupus patients who in the course of the disease presented with Hashimoto's thyroiditis. Methods A cohort of 10 patients, female, aged 21–42 years, suffering from SLE is presented. The patients were diagnosed with lupus and were either on treatment with hydroxychloroquine or with hydroxychloroquine and prednisone. Within this cohort a female patient aged 42 years had also antiphospholipid antibodies and had suffered a stroke at the age of 36. Results Within this cohort 6 patients had positive both anti-thyroglobulin and thyroid peroxidase antibodies, 3 patients had positive only anti-thyroglobulin antibodies and 1 patient had positive only thyroid peroxidase antibodies. Within this group, 7 patients were euthyroid and were followed up, while 3 had hypothyroidism and were on treatment with thyroxine. Conclusion In conclusion, SLE may be accompanied by Hashimoto's thyroiditis. In another cohort a two-fold increased risk of Hashimoto's thyroiditis was observed in lupus patients. The presence of anti-Sm antibodies was found to favor this association. In another cohort hypothyroidism, subclinical hypothyroidism and subclinical hyperthyroidism accompanied by the presence of thyroid autoantibodies was observed in a group of lupus patients. It appears that lupus patients may present with Hashimoto's thyroiditis with or without hypothyroidism and should be screened for this disorder during long-term observation.