This paper shows the results of an intralaboratory validation of a fast method for the determination of lipophilic shellfish toxins working under acidic conditions using ultra-high performance LC (UHPLC) with MS/MS. Fourteen lipophilic marine toxins and domoic acid were acquired with fast polarity switching. Whereas azaspiracids (AZAs), pecenotoxins, 13-desmethyl spirolide C (SPX1), and gymnodimine were analyzed in the positive mode, yessotoxins (YTXs) were measured in negative mode. The okadaic acid (OA) group compounds were analyzed in both positive and negative ionization modes, and the accuracy of the results for both were compared. When using dynamic multiple reaction monitoring (MRM) in fast polarity switching, LODs were lower and reproducibility and linearity were better compared to static MRM. The UHPLC separation allowed for higher sample throughput in routine use. Compared to the previously used HPLC/MSIMS method, LODs were improved up to a factor of 10 in mussel extract. Matrix effects were evaluated by comparing standards prepared in solvent with matrix-matched calibrations in blank mussel extract. For accurate quantification matrix-matched calibrations were used when analyzing reference mussel materials, providing recoveries for OA, Dynophysis toxins (DTX)1, DTX2, YTX, AZA1, and SPX1 between 80 and 120% with RSDs below 8% over a 3-day validation procedure.