We performed a retrospective analysis, of allogenic stem cell transplantation (allo-SCT) results, in 40 patients with diagnosis of acquired aplastic anemia or Fanconni Anemia, in a transplant center in Bogotá, Colombia, between 1996 and 2007. During that period, 42 transplants were performed in 40 patients. 28 (70%) acquired aplastic anemia and 12 (30%) Fanconni's Anemia. 17 (42.5%) female/25 (62.5%) male. Mean age was 22 years (4–57). Stem cells were obtained from peripheral blood in 36 (90%) and from bone marrow in 6 (15%). The majority of patients were of high risk; the mean time from diagnosis to transplant was 27.8 months (2–141) and 57.5% of them had received more than 20 transfusions before transplantation. Patients were conditioned with Cy-ATG in 24 (57.1%), high dose Cyclophosphamide (Cy) in 11 (26.2%), fludarabine-Cy-ATG in 3 (7.14%) and Alemtuzumab-Cy in 4 (9.52%). Mean CD34+ cell dose was 3.3 (1.08–6.66), TNC: 9.7 (1.2–59.2). Neutrophil engraftment was achieved at day +16 (3–54) post-transplantation. At a mean follow up of 19.5 months (7–128), overall survival is 65%. Comparison of results of different conditioning regimens shows that overall survival for patients conditioned with Cy alone is disappointing, 8/11 patients died, 6 due to GVHD and 2 due to infection. After adding ATG to Cy, mortality due to GVHD was significantly reduced. Only 7/24 patients died, GVHD was the cause of death only in 2. Infection was the cause of death in other 4. 2 patients had secondary graft failure, one died. The other received a second transplant and is alive with mixed chimerism, but free of transfusion support. Of 4 patients treated with alemtuzumab containing regimens, 3 had secondary graft failure, 2 died, and one received a second transplant successfully. On this group of patients Cy-ATG was the best conditioning regimen in terms of overall survival and GVHD incidence. The majority of patients in this cohort were remitted to transplant late in their disease, early treatment will probably improve the outcomes, as it has been confirmed in other papers.