Fusarium fungi are widely found in agricultural products, worldwide and can produce a great variety of mycotoxins. Fumonisins, produced by F. moniliforme, and deoxynivalenol, produced by F. graminearum, are two such mycotoxins that have received considerable attention as food safety concerns by regulatory agencies. High Performance Liquid Chromatography/Mass Spectrometry (HPLC/MS) was found to be a convenient analytical method to detect and quantify the naturally occurring fumonisin homologs and deoxynivalenol in extracts from grains and food products. The fumonisins are detected primarily as protonated molecules in the positive ion electrospray ionization (ESI) mode as they elute from a C-18 reverse phase column during a methanol water gradient containing acetic acid to facilitate chromatography. Deoxynivalenol can be detected as positive or negative ions in the atmospheric pressure chemical ionization (APCI) mode or in the negative ion ESI mode. One nanogram amounts of fumonisins or deoxynivalenol injected into the HPLC system are easily detected with signal to noise allowing detection limits of 1 microg g(-1) or better to easily be achieved with minimal clean-up of grain extracts.