A case of anti-mitochondrial antibody (AMA)-negative primary biliary cirrhosis (PBC) associated with painless thyroiditis is reported in a 47-year-old woman who diagnosed as PBC based on her elevated serum gamma-glutamyl transpeptidase and immunoglobulin M levels, as well as histological findings of destroyed bile ducts surrounded by mononuclear infiltrates in the biopsied liver. She was negative for AMA and had a depressed level of thyroid-stimulating hormone accompanied by increased free thyrosine, thyroxine and triiodothyronine levels and low titers of anti-microsomal and anti-thyroid peroxidase antibodies. Her thyroid disorder corresponded with painless thyroiditis. An association between PBC and hyperthyroidism is rare. Furthermore, an association between AMA-negative PBC and hyperthyroidism due to painless thyroiditis has not previously been reported.