With increased number of patients surviving on the long term, late effect after allogeneic hematopoietic stem cell transplantation have become of major clinical importance. Among these late effect, second malignancies have increasingly been recognized in the recent years. It has been usual to divide the problem of secondary malignancies following hematopoietic stem cell transplantation into three groups, i.e. leukemia, lymphoma and solid tumors. Recent clinical and biological data on these three types of malignancies, occurring after allogeneic stem cell transplantation, are summarized in this review. We will focus here only on second malignancies after allogeneic stem cell transplantation with particular emphasis on recent development on the pathogenesis, and early diagnosis, and treatment of these transplant-related complications.