Domoic acid (DA) is a marine neurotoxin that is somewhat unstable, particularly in acidic media. Several protocols were used to extract DA from naturally contaminated tissues of shellfish harvested in Portugal. A modified version of AOAC method no. 991.26, with a simplified 10 g extraction, was used and compared with an aqueous 50% methanol extraction. Mean recoveries were between 81 and 85% when extracts were analysed by LC on the same day of extraction. When acid extracts were frozen for 1 or 2 days recoveries lowered to 72%, and if injection was repeated on the following 3rd or 4th days only 57–65% was recovered. Relative standard deviation of recovery for these miscellaneous samples, which was between 10 and 13% on the day of extraction, increased approximately 10% each day the extract was reanalysed. On our regulatory monitoring work, we employ an aqueous 80% methanol extraction that is common with the lipid-soluble DSP toxins. We report here a mean recovery of 90±6% for this methodology. Our long-term stability studies of domoic acid in shellfish extracts showed that slow decomposition of this compound occur in filtered aqueous methanol extracts. Additionally, we also found that in frozen tissues slow decomposition is clearly observable over a time span of 1 month.