The validation of a method to identify and quantify methylmercury and ethylmercury by liquid-liquid extraction with hexane and determination by using gas chromatography coupled to mass spectrometry was evaluated. The method was validated according to EU Commission Decision 2002/657/EC. Certified reference materials NIST 2976 (mussel tissue) and NMIJ 7402-a (cod fish tissue) and an “in house” full matrix were used. Fractional factorial design was applied, whereas six experimental factors at two levels were employed. Analyses were carried out by two analysts and the intra-days and inter-days significance were considered, thus demonstrating that this method is adequate for the purpose in hand. The decision limits (CCα) and detection capability (CCβ) of the method were 13.88 and 14.55 μg L−1 for methylmercury and 15.74 and 16.07 μg L−1 for ethylmercury, respectively. Accuracy and precision were evaluated by means of recovery experiments at three concentration levels (20, 30, and 40 μg L−1), obtaining recoveries between 70 and 120 % and a coefficient of variation below 10 %. The validated method was successfully applied for determination of methylmercury and ethylmercury in canned tuna, fresh fish, and seafood samples obtained from local markets in Medellin, Colombia.