We tested the independent prognostic impact of two commonly used biomarkers, C-reactive protein (CRP) and interleukin-6 (IL-6), on allogeneic hematopoietic cell transplantation (HCT) outcomes. Consecutive patients who underwent a uniform reduced intensity regimen of fludarabine, melphalan and alemtuzumab were evaluated. Cryopreserved sera drawn before conditioning was available to measure CRP and IL-6 levels from 81 and 79 patients, respectively. Patients having CRP values above the median of 18.5 mg/L had significantly more grade 3 to 4 hepatic toxicity (P = 0.08), longer HCT hospital stay (P = 0.005), more aGVHD (P = 0.003), greater non-relapse mortality (NRM) (P =0.01) and inferior overall survival (P =0.02). Higher baseline CRP also correlated with more grade 3 to 4 infectious toxicity (P = 0.09). In contrast, pre-HCT IL-6 levels above the median of 78.3 pg/mL, did not confer a statistically significant increased risk of toxicities or mortality. Elevated hematopoietic cell transplantation-comorbidity index (HCT-CI) did not predict for any measure of HCT morbidity. After adjustment for disease status, comorbidity, performance status and age, elevated CRP concentration remained predictive of NRM. CRP holds promise as a readily available serum biomarker that can be measured prior to HCT conditioning to enhance estimates of transplantation tolerance.