Post-transplant lymphoproliferative disorders (PTLD) are morphologically/clinically heterogeneous. The main goal of this study was to define the histogenesis of PTLD (B-cell phenotype, EBV-related) in seven pediatric patients after allogeneic T-cell-depleted bone marrow transplantation. Immunohistochemical stains using histogenetic markers, including Bcl-6 (expressed by germinal center (GC) B cells), MUM1/IFR4 (late GC and post GC B cells), and CD138 (post GC B cells), were performed on paraffin-embedded tissue. By morphology, four cases were classified as polymorphic PTLD and three as monomorphic PTLD, according to the WHO classification. By the expression pattern of histogenetic markers, five cases (two polymorphic, three monomorphic PTLD) were of late GC/early post GC B-cell origin expressing only MUM1/IRF4. The remaining two cases (one monomorphic, one polymorphic PTLD) were of post GC B-cell origin expressing MUM1/IRF4 and CD138, but not Bcl-6. Our study indicates that histogenesis of PTLD may be defined by histogenetic markers using immunohistochemistry. The results suggest that most pediatric PTLD are of late GC/early post GC B-cell origin, and a minor group is of post GC B-cell origin. The histogenesis of PTLD appears independent of morphologic appearance. Further studies are warranted to confirm our observation and to evaluate the clinical significance of histogenetic pattern of PTLD.