Bone marrow transplantation (BMT) is recognized as a successful treatment for malignant and non-malignant hematological diseases. Thanks to transplantation, the number of long-term survivors has risen and with the improved prognosis a problem of ocular side effects has arisen. We carried out a retrospective study to determine the incidence and etiopathogenesis of ocular complications in a series of young patients undergoing BMT. One hundred children (62 males and 38 females) with a mean age of 7.12 (±3.3) years at the time of BMT (autologous in 66 cases, allogenic in 34) were followed for a mean of 4.2 years (range 2–9). The conditioning regimens preceding BMT induced cytoreductive chemotherapy alone (47 cases) or associated with total body irradiation (TBI) (53 cases) in three or six fractions for a total dose of 10–12 Gy. We examined every child before BMT and subsequently every six months. We did not include patients with ocular complications due to the primary disease. Thirty-three children showed several complications after BMT: 17 had subcapsular posterior cataract in both eyes and eight had tear hyposecretion; one had dramatic fungal panuveitis, four had hemorrhagic complications and five optic disk edema. TBI was significantly associated with the development of subcapsular posterior cataract.