Osteopenia is a complication of anorexia nervosa (AN) associated with a two- to three-fold increase in fractures. Nutritional deficits and hormonal abnormalities are thought to mediate AN-induced bone loss. Alterations in bone microarchitecture may explain fracture risk independent of bone mineral density (BMD). Advances in CT imaging now allow for noninvasive evaluation of trabecular microstructure at peripheral sites in vivo. Few data are available regarding bone microarchitecture in AN. We therefore performed a cross-sectional study of 23 women (12 with AN and 11 healthy controls) to determine hormonal predictors of trabecular bone microarchitecture. Outcome measures included bone microarchitectural parameters at the ultradistal radius by flat panel Volume CT (fpVCT); BMD at the PA and lateral spine, total hip, femoral neck and ultradistal radius by dual energy X-ray absorptiometry (DXA); and IGF-I, leptin, estradiol, testosterone and free testosterone levels. Bone microarchitectural measures, including apparent (app.) bone volume fraction, app. trabecular thickness, and app. trabecular number, were reduced (p<0.03) and app. trabecular spacing was increased (p=0.02) in AN vs. controls. Decreased structural integrity at the ultradistal radius was associated with decreased BMD at all sites (p=0.05) except for total hip. IGF-I, leptin, testosterone and free testosterone levels predicted bone microarchitecture. All associations between both IGF-I and leptin levels and bone microarchitectural parameters, and most associations between androgen levels and microarchitecture remained significant after controlling for body mass index. We concluded that bone microarchitecture is abnormal in women with AN. Endogenous IGF-I, leptin and androgen levels predict bone microarchitecture independent of BMI.