Presence of Stachybotrys chartarum in indoor environments has been linked to building-associated disease, however, the causative agents are unknown. Verrucarol (VER) and trichodermol (TRID) are hydrolysis products of some major S. chartarum mycotoxins, i.e. macrocyclic trichothecenes and trichodermin. We optimized gas chromatography-mass spectrometry (GC-MS) methods for detecting VER and TRID in S. chartarum-contaminated indoor environmental samples. Heptafluorobutyryl derivatives of both VER and TRID exhibited little MS fragmentation and gave much higher detection sensitivity (sub-picogram injected onto the GC column), both in GC-MS and GC-MSMS, than trimethylsilyl derivatives. Optimal detection sensitivity and specificity was achieved by combining chemical ionization and negative ion (NICI) detection with MSMS. With this method, VER and TRID were detected in building materials colonized by S. chartarum and TRID was demonstrated in dust settled in the breathing zone in a house where an inner wall was colonized. In summary, we have shown that NICI-GC-MSMS can be used to demonstrate mycotoxins in house dust in S. chartarum-contaminated dwellings.