Concentrations of paralytic shellfish toxins (C1+2, B1, dcGTX2+3, dcSTX, GTX2+3 and STX) were determined by LC-FLD in composite samples of digestive glands of the cockle Cerastoderma edule and in each sub-cellular particulate fractions obtained after differential centrifugation (nuclei+debris, mitochondria, lysosomes and microsomes). The specimens were sampled during the exposure to a bloom of Gymnodinium catenatum (day 0) and in the subsequent 8, 12, 14, 19, 21 and 25 days under natural depuration conditions. Toxin profiles of digestive glands were dominated by C1+2 followed by B1 and dcGTX2+3, although the proportion between C1+2 and B1 contents decreased with the time, indicating a slower elimination of B1. All toxins, except GTX2+3 and STX, were quantified in the four sub-cellular fractions. The content of the quantified toxins decreased most markedly in nuclei+debris and microsomal fractions, during the first eight and 12 days, respectively. Conversely, different patterns were observed among toxins in mitochondrial and lysosomal fractions. The less accentuated decreases of dcGTX2+3 and dcSTX contents in the mitochondrial fraction may have resulted from the conversion of other toxins, like C1+2 and B1, associated with enzymatic activities in that fraction. The largest discrepancy was registered in lysosomal fraction for B1, since its content increased after eight days of post-bloom conditions. Input of B1 may come from the conversion of other toxins, like the abundant B2 and C1+2. These transformations are associated to the major role of lysosomes in the intra-cellular digestive process of materials acquired through vesicular transport.