A simple and versatile procedure has been developed for the determination of selenium in biological samples for clinical purposes. The procedure consists of microwave sample digestion and the determination of selenium using atomic fluorescence spectrometry with a hydride generation system (HG-AFS). The method allows the determination of selenium in a range of 0.5–100.0 g with a detection limit not higher than 0.2 g and with good repeatability not exceeding 1%. It was applied for determination of selenium in women’s plasma samples (n = 90) with a suspicion of a thyroid cancer and the control group of women (n = 87). Most of the obtained results were in the range 30.0–60.0 g and either did not match the physiological level of selenium in human plasma or indicate moderate selenium deficiency. In the further examinations the thyroid tissues taken from 30 patients were analyzed. In most of the cases the selenium concentration was found to be lower (0.14–1.67 g wet weight) than its physiological level in a healthy tissue. On this basis the hypothesis has been drawn that selenium can be considered as an additional marker of the thyroid cancer disease.