In sesame seeds, high concentrations of lignans are present. When these lignans are fermented in the human colon, a range of structurally different lignans is formed. A good liquid chromatography/mass spectrometry (LC/MS) protocol for the analysis of lignans in complex mixtures is lacking. In order to develop such a protocol, electrospray ionization (ESI)-MS and atmospheric pressure chemical ionization (APCI)-MS, both in the positive and negative ionization mode, were compared. An extract from defatted sesame meal was analyzed by APCI-MS and ESI-MS, before and after deglucosylation. APCI-MS was found to be a more generic method than ESI-MS because lignans, especially sesamolin, sesamin and pinoresinol, were better detected by APCI-MS than by ESI-MS. Positive and negative ionization modes had to be combined in order to detect all lignans in a bacterial culture grown on aglyconic, acid-treated lignans from sesame oil and defatted sesame meal. Lignans with methylenedioxy-bridged furanofuran structures mostly lack phenolic hydroxyl groups and were, therefore, optimally detected in positive ionization mode. Dibenzylbutadiene lignans, which were formed during fermentation, carry hydroxyl groups and were better detected in negative ionization mode.