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A magnetic molecularly imprinted silica solid was obtained by sol-gel polymerization for the separation of domoic acid. The solid showed rapid adsorption kinetics with an adsorption equilibrium time of 5 min. The solid showed affinity to domoic acid under the interference of tryptophan and could be repeatedly used for 5 times at least. The solid was used as a solid-phase-extraction sorbent for the extraction of domoic acid from clam samples before measurement with liquid chromatography. The detection limit of 0.20 mg kg−1 was lower than the allowable limits in several countries or areas. The recoveries in the spiked samples were 88% approximately.