Purpose Anorexia nervosa (AN) is associated with reduced bone mass and an increased fracture risk. The aim was to evaluate the vitamin D status and the association with body mass index (BMI), fat mass and bone mineral density (BMD) in patients with severe AN during a prospective intervention study of intensive nutrition therapy. Methods This study comprised 25 Swedish female AN patients (20.1 +/- 2.3 years), who were treated as inpatients for 12 weeks with a high-energy diet. Serum 25-hydroxy-vitamin D (25(OH) D), calcium, phosphate and parathyroid hormone (PTH) were measured. BMD and body composition were assessed by dual-energy X-ray absorptiometry at study start and after 12 weeks. Results Twenty-two patients completed the study. The mean weight gain was 9.9 kg and BMI (mean +/- SD) increased from 15.5 +/- 0.9 to 19.0 +/- 0.9 kg/m(2), P amp;lt; 0.0001. Fat mass increased from median 12 to 27 %. The median serum 25(OH) D level was 84 nmol/L at baseline, which decreased to 76 nmol/L, P amp;lt; 0.05. PTH increased from median 21.9 to 30.0 ng/L, P amp;lt; 0.0001. BMC increased during the study period, P amp;lt; 0.001. Conclusions Serum 25(OH) D levels were adequate both at study start and completion, however, nominally decreased after the 12-week nutritional intervention. PTH increased subsequently, which coincide with the decreased 25(OH) D levels. The reduction in 25(OH) D could be due to an increased storage of vitamin D related to the increase in fat mass since vitamin D is sequestered in adipose tissue.