Objective: To examine the relationship between endogenous cortisol and bone, and the role of genetic variations in the glucocorticoid receptor (GR). Design and patients: The Longitudinal Ageing Study Amsterdam (LASA), a population-based cohort study in older men and women. Measurements: Serum fasting cortisol was assessed by competitive immunoassay (n = 1214); bone mineral density (BMD) by dual X-ray absorptiometry (DXA) (n = 502); broadband ultrasound attenuation (BUA) by ultrasound (n = 1209); fractures by self-report (n = 1211); and GR gene polymorphisms (ER22/23EK, N363S, 9beta, BclI) were genotyped by Taqman (n = 858). Results: Higher serum fasting cortisol was significantly associated with lower BMD at all sites and BUA at the heel in women, although most relationships were attenuated by age and body mass index (BMI). The effect on femoral neck BMD remained statistically significant in the fully adjusted model (r = -0.135, P = 0.04). No significant associations in men were found. Female 9beta G-allele carriers had 50.2 nmol/l lower cortisol and 1.2 lower free cortisol levels than AA homozygotes [P = 0.01 for (free) cortisol]. Furthermore, female BclI GG homozygotes had 54.8 nmol/l higher cortisol levels than C-carriers (P = 0.03). In the total population, BclI GG homozygotes had 0.05 g/cm 2 lower trochanteric region BMD (P = 0.03). For the other GR gene polymorphisms, no significant associations were found. Conclusions: Higher cortisol levels are associated with lower femoral neck BMD in elderly women. The G allele of the 9beta polymorphism was associated with lower serum cortisol levels in women. Female BclI GG homozygotes had higher serum cortisol levels, and BclI GG homozygotes had lower trochanteric region BMD in the total population.