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Inclusion criteria(suitable candidates are patients with chronic GVHD that meets NIH Consensus Working Group Guidelines in one of the following categories): (a) Previously untreated (newly diagnosed)high-risk patients with one or more of the following: platelets less than 100,000, greater than 50 percent skin involvement, bronchiolitis obliterans, receiving prednisone greater than or equal to 0.5 mg/kg/day (or equivalent) at the time of cGVHD diagnosis. (b) Previously treated high-risk (meeting the above definition) patients that have received initial therapy but are inadequately responding after less than or equal to 12 weeks of initial therapy with prednisone greater than or equal to 0.5 mg/kg/day or greater and/or CNI ± additional non-sirolimus agent (started at the time of chronic GVHD diagnosis), OR, previously treated standard-risk(not meeting the high risk criteria above) patients deemed inadequately responding after less than or equal to 12 weeks of initial therapy with prednisone greater than or equal to 0.5 mg/kg/day or greater and/or CNI. Note, additional systemic agents may not be started at the time of chronic GVHD diagnosis for patients with standard-risk chronic GVHD. (c) Weight greater than or equal to 25 kg. Exclusion criteria: (a) No evidence of chronic GVHD (for example, patients with late persistent acute GVHD or recurrent acute GVHD alone). (b) Inability to begin prednisone therapy at a dose of greater than or equal to 0.5 mg/kg/day. (c) Standard risk patients not treated with prednisone at 0.5-1 mg/kg/day and/or CNI as initial therapy. (d) Receiving sirolimus for treatment of chronic GVHD (sirolimus for prophylaxis or treatment of acute GVHD is acceptable). (e) Already receiving sirolimus (for prophylaxis or treatment of acute GVHD) with prednisone at greater than or equal to 0.25 mg/kg/day ± additional agents. (f) Receiving therapy for chronic GVHD for more than 12 weeks. (g) Invasive fungal or viral infection not responding to appropriate antifungal or antiviral therapies. (h) Creatinine clearance less than 50 mL/min/1.73 meters squared or a serum creatinine based on the Cockcroft-Gault formula (adults) or Schwartz formula (age less than 12 years). (i) Inability to tolerate oral medications. (j) Absolute neutrophil count less than 1500 per microliter. (k) Requirement for platelet transfusions other than to perform extracorporeal photopheresis. (l) Progressive or recurrent malignancy defined other than by quantitative molecular assays. (m) Known hypersensitivity to sirolimus.