Concentrations of the paralytic shellfish toxins C1+2, C3+4, B1, B2, dcGTX2+3, dcSTX, dcNEO, GTX2+3, GTX1+4, STX and NEO were determined by LC-FLD in composite samples of digestive glands and gills of Cerastoderma edule cockle. The specimens were sampled in Aveiro lagoon, Portugal, under natural depuration conditions (days 0, 8, 12, 14, 19, 21 and 25) after exposure to a bloom of Gymnodinium catenatum. Individual paralytic shellfish toxins indicated different pathways of elimination and biotransformation in digestive gland and gills. Toxin concentrations in gills were lower than in the digestive gland. Most of the quantified toxins in the digestive gland decreased during the 25 days of observation according to negative exponential curves, and only B1, B2 and NEO showed slight irregularities with the time. Concentrations of C1+2, C3+4 and dcGTX2+3 in gills decreased progressively with the time, however B1, B2 and dcSTX showed pronounced increases. Higher concentrations of those toxins in days 8 and 12 in comparison to the initial value (day 0) indicate conversion of other toxins into B1, B2 and dcSTX during those periods. It appears that inter-conversion of toxins occurs as G. catenatum cells are retained in gills before being transferred to other compartments.