In the context of the French Phytoplankton and Phycotoxins Monitoring Network (REPHY) programme, shellfish samples were harvested from different locations where harmful algae blooms were known to have occurred. For all shellfish samples found positive by the mouse bioassay for diarrhetic shellfish poisoning (DSP) toxins, liquid chromatography (LC) coupled with mass spectrometry (MS) was used to search for the following lipophilic toxins: okadaic acid (OA), dinophysistoxins (DTXs), pectenotoxins (PTXs), azaspiracids (AZAs), yessotoxins (YTXs), spirolides (SPXs) and gymnodimines (GYMs). In order to investigate the presence of acyl-OAs and/or acyl-DTX-1,-2 (DTX-3), alkaline hydrolysis was performed on all samples, and LC/ MS analyses were carried out on the samples before and after hydrolysis. The results revealed different lipophilic toxin profiles as a function of the shellfish sampling location. The primary finding was that all of the samples contained OA and acyl-OA. In addition, other lipophilic toxins were found in shellfish samples: DTX-2, acyl-DTX-2 and SPXs (SPX-A, SPX-desMeC) on the Atlantic coast (Southern Brittany, Arcachon), and pectenotoxins (PTX-2, PTX-2-seco-acid and 7-epi-PTX-2-seco-acid) on the Mediterranean coast (Thau lagoon, the island of Corsica). This paper reports on the first detection of PTX-2, SPX-A and their derivatives in French shellfish.