A method for the analysis of 12 perfluorinated compounds (PFCs) in human urine by ultra high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was developed and validated. One mL 2% formic acid in methanol was added into the urine. After ultrasonication and centrifugation, the samples were purified by a solid phase extraction column and examined by UPLC-MS/MS. The target compounds were quantified by stable isotope dilution technique. The linear range was 0.05 -50 microg/L for the 12 PFCs and the correlation coefficient > or = 0.992. The limits of detection of 12 PFCs were in the range of 0.44 - 3.47 ng/L. The matrix recoveries of the method for the 12 PFCs in three spiked levels (20, 100, 500 ng/L) ranged from 80.3% to 116.2%. The relative standard deviations (RSDs, n = 5) were between 5.5% and 13.8%. The sensitive and accurate method was successfully applied to the analysis of PFCs in human urine.