Selenium (Se) supplements have been used to control Kashin-Beck disease (KBD) for decades, but the effect of diet without Se supplements is unclear because the prevalence of KBD has decreased. This matched cohort study was undertaken to determine dietary factors affecting selenium nutrition status of children living in KBD areas and the effects of Se supplements in preventing KBD. A total of 593 children aged 5-12 years were randomly selected during the high prevalence period of KBD from 1992 to 1995. Children in one village received Se supplemented (Se+) salt and were matched with three children in 16 other villages who did not receive Se supplemented (Se-) salt. A questionnaire and determinations of occipital hair Se to reflect body Se status were obtained at baseline (April 1992), at 6 months (October 1992), and yearly each April through 1995. Hair Se content in the Se+ group was significantly higher than in the Se- group (P < 0.001) at all time-points and was significantly related to the incidence of suspected KBD symptoms (P = 0.018). Four dietary factors significantly affected hair Se contents. Se levels were increased by consumption of Se+ salt (P < 0.001) and eating meat/egg often (P = 0.019) or occasionally (P = 0.001). Se levels were decreased by consumption of grain mildewed at harvest or in storage (P < 0.001 for each) and drinking ditch, river, or cellar water (P < 0.001; P = 0.002; P < 0.001, respectively). These results show that Se+ salt had a significant effect in maintaining the Se nutrition status of children in this cohort study but that dietary factors in those without Se supplements contributed as well.