BACKGROUND Selenium (Se) has an essential role in thyroid hormone metabolism. It has the potential to play a major part in the outcome of iodine (I) deficiency The aim of the present study was to evaluate the Se and I status of biological samples (serum and urine) of 160 goitrous male (GMPs) and 195 female patients (GFPs). The supplemental effects of Se (200 microg/day) and I (100 - 125 microg/day) were evaluated after 6 months. For comparison purposes, non-goitrous subjects of both genders (n = 440) with same age group and socioeconomic status were also selected. METHODS Hydride generation atomic absorption spectrometry (HGAAS) was used to investigate the Se concentration in the biological samples, prior to microwave assisted acid digestion. Quality control for the methodology was established by comparing the results obtained with certified samples with those obtained by conventional wet acid digestion method on the same CRMs and real samples. RESULTS The mean serum Se concentration was significantly lower, while urinary Se was higher in GMPs and GFPs as compared to control subjects (p < 0.005 and < 0.007, respectively). The levels of I, free tri-iodothyronine, and thyroxin were found in goitrous patients of both genders were low compared to age matched healthy controls (p < 0.015, < 0.006, and < 0.002, respectively). On the other hand, high levels of thyroid stimulating hormone were observed in GMPs and GFPs (p < 0.009). CONCLUSIONS It was observed that Se in biological samples of hypothyroid patients can play an important role in determining the severity of the hypothyroidism associated with iodine deficiency. A wide-scale epidemiological study is recommended together with the examination of the potential preventive role of Se supplementation in endemic goiter regions.