Allogeneic hematopoietic cell transplantation (HSCT) is considered a curative treatment for acute myelogenous leukemia (AML). Extramedullary relapse after HSCT for AML is a rare event and is less well defined than systemic, hematologic relapse. We retrospectively studied all patients with AML (n = 436) who underwent HSCT at the University of Minnesota between 1996 and 2008 who developed either a bone marrow (BM) or extramedullary (EM) relapse, and examined the incidence and risk factors for BM and EM relapse. Of 128 patients who relapsed post-HSCT, 25 had relapse in EM sites, either isolated (n = 13) or with concurrent BM relapse (n = 12). Relapse sites included bone (n = 1), central nervous system (n = 6), gastrointestinal (n = 4), lymphatic (n = 4), skin (n = 5), genitourinary (n = 1), pulmonary (n = 1), and soft tissue (n = 3). The time to relapse was longer in the EM sites (median, 328 days vs 168 days). Patients with EM relapse were more likely to have had preceding acute graft-versus-host disease (GVHD) (77% vs 49%; P = .03) or chronic GVHD (46% vs 15%; P = .02) compared with those with BM relapse. The 6-month survival postrelapse was significantly better in patients with isolated EM relapse (69%) compared with those with combined EM and BM relapse (8%) or those with BM relapse alone (27%) (P < .01). Compared with local therapy alone, systemic therapy yielded better 6-month survival in patients with EM relapse. This study suggests differing pathogenesis of BM relapse versus EM relapse of AML after allogeneic HSCT. GVHD and its accompanying graft-versus-leukemia effect may better protect BM sites, but patients with EM relapse have better responses to combined therapy and improved survival compared with those with BM relapse. Copyright © 2012 American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.