OM is a frequent complication for patients undergoing HSCT. The aim of this study was to evaluate the possible risk factors for OM in children undergoing HSCT for PI. A retrospective study was carried out on 55 consecutive medical records of patients with PI (including osteopetrosis) who underwent HSCT. Age at the time of HSCT, gender, diagnosis, type of donor, conditioning regimen, engraftment, graft‐versus‐host disease, and severity and duration of OM were collected at the beginning of the conditioning until day 100 post‐HSCT or death. OM was measured using the WHO scale. Patients' age range at the time of HSCT was quite wide; 59.2% of the patients who were under nine months (n = 13) developed OM vs. 87.8% of the patients older than nine months (n = 29) (p = 0.01). T‐cell positive patients had a statistically significant higher risk of developing OM (p = 0.04), as did those receiving a more intensive conditioning regimen (p < 0.01). PI patients undergoing HSCT are at higher risk of developing OM if the PI is a T‐lymphocyte‐positive disease and/or if the HSCT recipient is over nine months of age.