The biotoxins, azaspiracids (AZAs), from marine phytoplankton accumulate in shellfish and affect human health by causing severe gastrointestinal disturbance, diarrhea, nausea and vomiting. Specific and sensitive methods have been developed and validated for the determination of the most commonly occurring azaspiracid analogs. An LTQ Orbitrap mass spectrometer is a hybrid instrument that combines linear ion trap (LIT) mass spectrometry (MS) with high-resolution Fourier transform (FT) MS and this was exploited to perform simultaneous ultra-high-resolution full-scan MS analysis and collision-induced dissociation (CID) tandem mass spectrometry (MS/MS). Using the highest mass resolution setting (100 000 FWHM) in full-scan mode, the methodology was validated for the determination of six AZAs in mussel (Mytilus galloprovincialis) tissue extracts. Ultra-high mass resolution, together with a narrow mass tolerance window of ±2 mDa, dramatically improved detection sensitivity. In addition to employing chromatographic resolution to distinguish between the isomeric azaspiracid analogs, AZA1/AZA6 and AZA4/AZA5, higher energy collisionally induced dissociation (HCD) fragmentation on selected precursor ions were performed in parallel with fullscan FTMS. Using HCD MS/MS, most precursor and product ion masses were determined within 1ppm of the theoretical m/z values throughout the mass spectral range and this enhanced the reliability of analyte identity. For the analysis of mussels (M. galloprovincialis), the method limit of quantitation (LOQ) was 0.010μg/g using full-scan FTMS and this was comparable with the LOQ (0.007μg/g) using CID MS/MS. The repeatability data were; intra-day RSD% (1.8-4.4%; n=6) and inter-day RSD% (4.7-8.6%; n=3). Application of these methods to the analysis of mussels (M. edulis) that were naturally contaminated with azaspiracids, using high-resolution full-scan Orbitrap MS and low-resolution CID MS/MS, produced equivalent quantitative data. © 2010 John Wiley & Sons, Ltd.