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We investigated, with quantitative HPLC/mass spectrometry, the selenium metabolites in urine from five cancer patients receiving high doses of l-selenomethionine over an extended period (2 × 4000 μg Se/day for 7 days, then 4000 μg Se/day for 21 days) as an adjunct to their normal cancer chemotherapy. Urine samples were collected at day 0 (all 5 patients), and at 2–3 additional collection times ranging from 1 to 33 days. The background selenium concentrations ranged from 12 to 55 μg Se/L and increased to 870 to 4420 μg Se/L for the five patients during the study. All five patients had appreciable levels of selenosugars in their background urine sample, and the concentrations increased dramatically after selenium intake. Trimethylselenonium ion (TMSe), on the other hand, was generally present as only a trace metabolite in background urine, and, although the concentration of TMSe increased following selenium exposure, it became a less significant proportion relative to selenosugars. These data refute the currently accepted role of TMSe as the preferred excretion metabolite when selenium exposure is high.