Although host LTi cells were radiosensitive, we observed an initial trend for greater LTi cell persistence compared with controls as well as a transient increase in the frequency of a CD45–VCAMhiICAMhi population akin to the phenotype of activated LTo-like cells; however, neither population was sustained and both cell types were severely depleted compared with no-GVHD controls at later time points. Here, PTPRC is linked to graft versus host disease.