Hypertension and diabetes are frequent early complications of allogeneic hematopoietic cell transplantation (HCT); however, their long-term outcomes are not well known. We conducted a retrospective cohort study to describe the risk factors and natural history of post-HCT hypertension and diabetes in 180 consecutive adult (n = 106) and pediatric (n = 74) allogeneic HCT recipients from 2003-2005 who had survived for 1 year post-HCT. The pediatric patients were less likely than the adult patients to have pre-HCT hypertension and diabetes, smoking history, or high-risk disease and more likely to receive myeloablative (MA) conditioning. All patients were followed until at least 2 years post-HCT; of these 1-year survivors, 156 (87%) were alive at 2 years. Acute or chronic graft-versus-host disease (aGVHD, cGVHD) occurred in 118 (66%) patients; of these, 24% received cyclosporine (CsA) for >12 months and 47% received prednisone for >12 months. Within 2 years post-HCT, 126 (70%) had hypertension and 54 (30%) had diabetes. Rates were similar for the adult recipients (hypertension, 68%; diabetes, 30%) and the pediatric recipients (hypertension, 73%; diabetes, 30%). At 2 years post-HCT, in the patients with hypertension, hypertension had not resolved in 34%, and among patients with diabetes, diabetes had not resolved in 32%. On multivariate analyses, exposure to CsA increased the risk of developing hypertension post-HCT (relative risk, 1.6; 95% confidence interval [CI], 1.1-2.5; P = .03), but did not affect its persistence at 2 years. Exposure to high-dose corticosteroids (cumulative prednisone dose of > 0.25 mg/kg/day) increased the likelihood of developing diabetes (relative risk, 3.6; 95% CI, 1.7-7.5; P < .01) and for having persistent diabetes at 2 years post-HCT (relative risk, 4.1; 95% CI, 1.0-18.2; P = .05). Hypertension and diabetes are frequent early complications of allogeneic HCT, but subsequently resolve in a large proportion of recipients in the first 2 years after transplantation. Continued monitoring and treatment of hypertension and diabetes is necessary in allogeneic HCT survivors, especially in those exposed to high doses of corticosteroids.