The Thai medicinal plant Mitragyna speciosa (kratom) is misused as a herbal drug. Besides this, a new herbal blend has appeared on the drugs of abuse market, named Krypton, a mixture of O-demethyltramadol (ODT) and kratom. Therefore, urine drug screenings should include ODT and focus on the metabolites of the kratom alkaloids mitragynine (MG), paynantheine (PAY), speciogynine (SG), and speciociliatine (SC). The aim of this study was to develop a full-scan gas chromatography-mass spectrometry procedure for monitoring kratom or Krypton intake in urine after enzymatic cleavage of conjugates, solid-phase extraction, and trimethylsilylation. With use of reconstructed mass chromatography with the ions m/z 271, 286, 329, 344, 470, 526, 528, and 586, the presence of MG, 16-carboxy-MG, 9-O-demethyl-MG, and/or 9-O-demethyl-16-carboxy-MG could be indicated, and in case of Krypton, with m/z 58, 84, 116, 142, 303, 361, 393, and 451, the additional presence of ODT and its nor metabolite could be indicated. Compounds were identified by comparison with their respective reference spectra. Depending on the plant type, dose, administration route, and/or sampling time, further metabolites of MG, PAY, SG, and SC could be detected. The limits of detection (signal-to-noise ratio of 3) were 100 ng/ml for the parent alkaloids and 50 ng/ml for ODT. As mainly metabolites of the kratom alkaloids were detected in urine, the detectability of kratom was tested successfully using rat urine after administration of a common user's dose of MG. As the metabolism in humans was similar, this procedure should be suitable to prove an intake of kratom or Krypton.