The aim of the study was to examine bone density and architecture with three different measurement methods in a sample of young women with anorexia nervosa (AN) and in an age-matched control group of women. Three-dimensional periphery quantitative computer tomography (3D-pQCT) at the ultradistal radius, a new technology providing measures of cortical and trabecular bone density and architecture, was performed, as well as quantitative ultrasound (QUS) at the heel, and dual energy X-ray absorptiometry (DXA) at the spine and hip. Thirty-six women with AN aged 18-30 years (mean duration of AN: 5.8 years) and 30 age-matched women were assessed. Bone mineral density measured by DXA at the spine and hip, and broadband ultrasound attenuation measured by QUS at the heel were significantly lower in patients than controls. 3D-pQCT demonstrated a highly significant deficit in the absolute number of bone trabecules and a significant reduction of cortical thickness. Severity of underweight was significantly associated with bone deficits at the hip measured by DXA. 3D-pQCT revealed mostly deficits of cortical bone related with age of onset of eating disorder. Using three different methods to measure bone density and bone structure at the hip, spine, heel and ultradistal radius, significant deficits in bone mineral density both in trabecular and cortical bone, as well in trabecular structure could be demonstrated in the AN patients.