Permanent alopecia after haematopoietic stem cell transplantation (HSCT) is distressing and few studies have investigated this late effect. The aim of the study was to assess the percentage of patients with alopecia and investigate risk factors for alopecia. Patients who underwent allogeneic HSCT before age 19 years, from January 1990 to January 2013, who were at least 2 years after transplant and in follow-up in our clinic were included. Alopecia was defined as clinically apparent decreased hair density. Possible risk factors considered for alopecia after HSCT included: gender, age, diagnosis, donor type, conditioning regimen: cranial irradiation (TBI/cranial radiotherapy) and/or chemotherapy, which chemotherapeutic agents were used and acute/chronic GvHD. The percentage of permanent alopecia in our cohort was 15.6% (41/263 patients). All patients had diffuse alopecia except for one with alopecia totalis. In multivariate analysis, a conditioning regimen with busulphan and busulphan plus fludarabine (odds ratio (OR) 5.7 (confidence interval (CI): 2.5–12.7) and OR 7.4 (CI: 3.3–16.2), respectively, was the main risk factor and associated with alopecia independent of acute/chronic GvHD. Neither TBI nor other alkylating chemotherapy, including treosulfan, was associated with alopecia. In conclusion, permanent alopecia after HSCT is associated with busulphan and GvHD and occurs in 16% of patients.