Objective To observe the effects of pentabrominated diphenyl ether (BED-99) on the histological structure and function of the thyroid of rats. Methods Forty SPF, SD rats aged 4 weeks, were randomly divided into 4 groups according to the body weight,10 in each group. The rats were treated with BED-99 at the doses of 30 mg/kg,60 mg/kg,120 mg/kg,respectively, through gavage. The rats in the control group were received the equal volume of corn oil. The levels of serum hormone were determined,the change of histopathology,histochemistry and follicular cells ultramicroscopic structure were observed at 15 days of exposure to BED-99. Results Serum levels of thyroxin (FT4),triiodothyronine (FT3),decreased gradually with dose increase at 15 days of exposure to BED-99.However,thyroid stimulating hormone (TSH) levels increased. The thyroid follicular epithelium hyperplasia was aggravated gradually with dose increase. Proliferating cell nuclear antigen (PCNA) positive cells increased constantly with dose increase. The activities of thyroperoxidase (TPO) and succinate dehydrogenase (SDH) of the treated rats increased significantly compared with the controls,and appeared color darkened. The rough endoplasmic reticulum of the thyroid follicular cells changed to saccate under the electron microscope,whereas nucleolus,cell membrane and mitochondria were not injured. Conclusion BDE-99 may damage the histological structure and function of the thyroid, the mechanism may be that BDE-99 down-regulates the thyroglobulin synthesis and then induces thyroxin level decrease which causes an increase of TSH through feedback.