Mice deficient in the runt homology domain transcription factor Runx1 die of severe anemia in utero by embryonic day (E)12.5. A reactivatable Runx1 knockout embryonic stem cell (ESC) and mouse systems were generated by the targeted insertion of a loxP-flanked multipartite gene stop/trap cassette designed to simultaneously ablate the expression of Runx1 and report on the activity of its promoters. The cassette's in-frame LacZ reporter enabled activities of the proximal and the distal promoters to be differentially monitored. Although Runx1-null ESCs were capable of primitive erythroid differentiation in vitro, their capacity to generate granulocyte/macrophage or mixed myelo-erythroid embryoid bodies was lost. Cre-mediated reactivation restored Runx1 structural integrity and rescued the hematopoietic differentiation potential of ESCs. Mice with the reactivated allele survived, showed no hematopoietic deficit, and expressed all major splice isoforms of Runx1 appropriately. This multipurpose mouse model will be useful for the analysis of the critical Runx1-dependent check-point(s) in hematopoietic development. genesis 44:115–121, 2006. © 2006 Wiley-Liss, Inc.