Mercaptoundecahydrododecaborate (BSH) is an important agent in boron neutron capture therapy (BNCT) of various cancers. A simple and rapid analytical method for the measurement of mercaptoundecahydrododecaborate in aqueous solution and in urine by Fourier transform infrared spectroscopy has been developed. A thin-pathlength sampling apparatus was used to minimize the strong absorption of water. The subtraction of water absorbance from sample spectra resolved a B-H band at 2493 cm-1. The quantitative measurement of BSH concentration was carried out by integrating the B-H band above baseline in the range of 2534-2440 cm-1. The lower limit of measuring the concentration of sodium BSH (Na2B12H11SH) in our experiment was 10 micrograms/ml (about 5 ppm of boron). This method measures the hydroborate (B-H) concentration instead of total boron and, thus, may be utilized to measure the BSH concentration in in vivo samples for metabolic studies.