There have been many advances in the field of stem cell transplantation over the past few years. Newer preparative regimens and better supportive care measures are allowing more children to survive and lead long lives after stem cell transplantation. We are only now beginning to see what the cost of this success may be in regard to the long-term effects of this treatment. Most long-term follow up studies have been reported in the adult literature and there is very little information on the pediatric population. Children who undergo stem cell transplantation will have a long period of observation in which new and different complications can occur. This article looks at the current literature on secondary malignancies and lymphoproliferative disorders after stem cell transplantation in children, with particular focus on risk factors, possible strategies for prevention, and treatment.