A rapid method for the detection of marine toxins was developed using an ultra-performance liquid chromatography (UPLC) system coupled to a latest generation mass spectrometry (MS) system. The analysis of 21 lipophilic marine toxins was achieved on an Acquity C18 column using a water-acetonitrile gradient with a cycle time of 6.6 min, reducing analysis time by more than a factor two compared to HPLC while maintaining peak resolution. Linear ranges, limits of detection and limits of quantification were established for okadaic acid (OA), pectenotoxin-2, azaspiracid-1 (AZA1), yessotoxin, gymnodimine and 13-desmethylspirolide C. The method was found to be accurate when using a triplicate methanolic extraction. Matrix effects were assessed by standard addition of OA and AZA1 in extracts of raw and heat-treated flesh of mussels and oysters. For the analysis of AZA1, the UPLC-MS method was always prone to signal suppression, while for OA analysis signal suppression was observed in extracts of raw shellfish flesh and signal enhancement in extracts of heat-treated flesh. Matrix effects occurring in the method presented are diminished compared to previous studies.