This prospective study examines bone density and structure over a two-year time period in women with anorexia nervosa (AN) under weight gain treatment. Twenty-four women with AN were examined at baseline and at two annual follow-up examinations. In 9 AN patients BMI increased whereas in 15 it remained unchanged or decreased. Dual energy X-ray absorptiometry (DXA) was performed on the lumbar spine, the femoral neck and the whole hip and three-dimensional peripheral quantitative computer tomography (3D-pQCT) was performed on the ultradistal radius. ANOVAs for repeated measures were used to examine change over time in BMI and bone parameters. At baseline, patients with increased BMI had significantly higher bone density of femoral neck and total hip, and higher levels in all 3D-pQCT parameters of the ultradistal radius, compared to the group with unchanged or decreased BMI. The two groups did not differ at baseline in bone density of the spine. ANOVAs showed that bone density of the total hip increased significantly and that overall bone density (D100), the density of the trabecular area (D.Trab.) and the cortical thickness (C.Th.) in the ultradistal radius decreased significantly. Group x time interactions showed that changes over time were different in the two groups with regard to spine density and in the parameters D100, D.Trab. and C.Th. of the ultradistal radius. In the group with increased BMI the spine density dropped at the first follow-up whereas at the second follow-up it rose again to baseline. Patients with unchanged or decreased BMI showed a small but steady increase in spine density. The group changes of D100, D.Trab. and C.Th. of the ultradistal radius all followed the same pattern. Bone mineral density at all locations measured with both technologies (DXA and 3D-pQCT) did not vary according to BMI changes. The course of bone density and structure at different locations was different, and, despite weight increase, bone regain appeared to need different time periods.