To evaluate the feasibility of urine perchlorate as a biomarker of ammonium perchlorate (AP) exposure and to explore the correlation between the thyroid function indicators and the perchlorate concentrations, a sensitive and selective ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) method was developed to detect perchlorate in urine samples. Rats were orally administrated with different doses of perchlorate. Serum free thyroxine (FT4), free triiodothyronine (FT3), and thyroid-stimulating hormone (TSH) were determined by radioimmunoassays. The results showed that a dose of AP up to 520 mg kg(-1) body weight induced a significant increase of TSH, with a decrease of FT4. Particularly, the levels of urine perchlorate increased dose-dependently on AP exposure from drinking water. The findings highlighted that urine perchlorate may be a useful biomarker for AP environmental exposure.