Background Kallmann syndrome (KS) is a rare genetic condition characterized by congenital early-onset hypogonadotropic hypogonadism and anosmia or hyposmia. Male subjects are more frequently affected and present absent/delayed puberty, low testosterone levels with higher risk for osteoporosis. Therefore, to maintain normal levels of sex steroids and prevent bone loss, male KS needs life-long hormonal replacement therapy (HRT). Aims The objective of our study is to assess bone involvement in subjects with KS currently treated with HRT. Methods In our retrospective study, we analyzed data from medical records of patients with KS treated with HRT (either gonadotropins or testosterone preparations), including clinical history, biochemical parameters, and the following outcome measures: the bone mineral density (BMD) at the lumbar spine (LS), femoral neck (FN), and total body less head (TBLH); and the Vertebral Fracture Assessment (VFA) by Dual Energy X-ray Absorptiometry (DXA). Results Clinical and instrumental data of 32 patients with KS were evaluated; their mean age was 30.32 (+/- 10.09) years, their mean body mass index (BMI) was 25.71 (+/- 3.23) kg/m(2). Four patients (12.5 %) had a LS BMD Z score below the expected range for age. Five patients had vertebral deformities observed at VFA. Duration of HRT was related to bone health parameters: BMD at all measured sites were higher in patients receiving adequate HRT for more than 2 years compared with the patients treated for less than 6 months. A deficient vitamin D status was found in 43 % of cases and it was prevalent in patients with shorter HRT. Discussion and conclusion Early starting and adequate duration of HRT are related to bone health parameters in patients with congenital hypogonadotropic hypogonadism due to KS. Restoring vitamin D sufficiency might also be advisable in this condition.