Electrospray ionization (ESI) high-performance liquid chromatography/mass spectrometry using both ion trap and triple quadrupole mass spectrometers has been utilized for the detection and characterization of fumonisin mycotoxin impurities in a purified sample of fumonisin B1 (FB1). Multi-stage tandem mass spectrometry (MSn) and liquid chromatography/tandem mass spectrometry (LC/MS/MS) of FB1 and the fifteen synthetically prepared methyl esters of FB1 on the ion trap instrument allowed investigation of the numerous fragmentation pathways available for this compound class. Data-dependent LC/MS/MS precursor-ion scan to product-ion scan experiments, based on the ion trap MSn experiments, were carried out on a triple quadrupole instrument and facilitated the detection of twelve, and the structural characterization of eight, minor impurities on the purified sample of FB1. Data-dependent LC/MS/MS full scan to product-ion scan experiments on the ion trap instrument resulted in the detection and characterization of fifteen further impurities in the purified sample of FB1; this number included the four uncharacterized impurities detected in the triple quadrupole LC/MS/MS experiments.