The development of a liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for the simultaneous determination of 16 mycotoxins possibly related to the ‘Sick Building Syndrome’ on filters and in fungal cultures is described. Fungi-surface sampling as regards the ‘Sick Building Syndrome’ preferably happens by scraping off fungal material and vacuuming onto cellulose filters. Therefore, these two media were used as samples. They were spiked with nivalenol, deoxynivalenol, zearalenone, diacetoxyscirpenol, T-2 toxin, verrucarol, verrucarin A, neosolaniol, sterigmatocystin, roridin A, ochratoxin A, aflatoxin B1, aflatoxin B2, aflatoxin G1 and aflatoxin G2, which can be produced by isolates from fungi-damaged buildings. Deepoxy-deoxynivalenol was used as internal standard. Samples were extracted with organic solvents and the different mycotoxins were separated by high-performance liquid chromatography (HPLC) using a C18 reversed-phase SunFire analytical column and a mobile phase of variable mixtures of ammonium acetate (10 mM) and sodium acetate (20 µM) in water (solvent A) and in methanol (solvent B). The samples were run on-line with a Micromass Quattro Micro triple quadrupole mass spectrometer in positive electrospray ionisation mode using multiple reaction monitoring (MRM). The detection limits of the procedure varied from 50 to 0.009 pg/µL for filter samples and from 75 to 0.04 pg/µL for fungal culture samples. As the method includes few and non-labourious sample treatment steps, it should allow for a high throughput of samples. Copyright © 2006 John Wiley & Sons, Ltd.