More than 250 toxic substances, including pesticides and mycotoxins, have been identified and quantified in ginkgo biloba nutraceutical products using liquid chromatography (LC) coupled to high resolution mass spectrometry (Exactive-Orbitrap). A “dilute and shoot” procedure, using acetonitrile with formic acid (1% v/v), was applied for the extraction of the target compounds. In this case, after this procedure, a clean-up step was necessary using a mixture of sorbents (PSA, GBC, C18 and Z-Sep+). Parameters such as trueness, repeatability, intermediate precision, limits of detection and quantification were evaluated. Recoveries between 70 and 120% with relative standard deviation (RSD) values lower than 20% were obtained for 260 of the compounds. Limits of detection and quantification below 5 and 10μgkg−1 were obtained, respectively. Nine samples of ginkgo biloba nutraceutical products were analyzed, finding pesticides in 8 out of 9 samples, such as hymexazol (10μgkg−1) and tebufenozide (55–459μgkg−1). In the case of mycotoxins, aflatoxin B1 (5–54μgkg−1), aflatoxin B2 (4–300μgkg−1) and T-2 toxin (18–20μgkg−1) were found in 6 samples.