The chemical purity of two synthetic 4-boronophenylalanine (BPA, C 9 H 12 O 4 BN) batches produced by two different pathways were investigated by high performance liquid chromatography/electrospray mass spectrometry. Currently, BPA is one of the most important clinical boron carriers in boron neutron capture therapy (BNCT). Low energy tandem mass spectrometry was used to elucidate the structure of BPA and two minor signals eluting later than the major compound. In the mass spectrom a very intense singly charged [MH] ion m/z 209 was observed. The ratio of 10 B/ 11 B was estimated also. The product-ion spectrum of BPA shows distinct losses of 18, 46 and 89 u. Based on the fragmentation of the major compound two impurities were characterized. In both cases an intense molecular ion, 244 u and 285 u was observed. Knowing the synthetic pathway and fragmentation of the major compound we suggest the following formulae for the impurities: C 9 H 10 O 2 BrN and C 15 H 16 O 4 BN. Further evidence to the first impurity is the detected isotope pattern, corresponding to bromine. The existence of the impurities can be explained and avoided by exploring the synthetic pathways used. High performance liquid chromatography/electrospray mass spectrometry was demonstrated to be an important novel analytical instrument to check the purity of BPA prior to clinical studies in BNCT.