Sepsis is one of the medical emergencies, and its early detection, within the first hours of development, and proper management improve outcomes. Molecular diagnostic assays using whole blood collected from patients with suspected sepsis have been developed, but the decision making is difficult because of the possibility of false positives, due to contamination. Here, we evaluated the performance of the reverse blot hybridization assay (REBA) Sepsis-ID test for the detection of sepsis-causing microorganisms using whole-blood samples. In addition, the concentrations of Creactive protein (CRP) and procalcitonin (PCT) were determined to evaluate whether these biomarkers can provide criteria for performing REBA Sepsis-ID in clinical settings. For this study, EDTA-anticoagulated whole blood was simultaneously collected for REBA Sepsis-ID and blood culture from 440 patients with suspected sepsis, from January to October 2015. In addition, CRP and PCT concentrations were measured in 227 patients. The overall positive rates of REBA Sepsis-ID and blood culture were 16.6% (73/440) and 13.9% (61/440), respectively. The pathogen-positive rates of REBA Sepsis-ID and blood culture were 9.8% (43/440) and 9.5% (42/440), respectively. The areas under the receiver operating characteristic (AUROC) curves of PCT and CRP for predicting pathogen-positive results of REBA Sepsis-ID were 0.72 and 0.69, respectively. The PCT concentrations in the group of patients aged ≥50 years were significantly higher than those in the group aged <50 years. After adjusting for age, the PCT AUROC value was 0.77 for predicting pathogen-positive results of REBA Sepsis-ID. The optimal cutoff values of PCT concentrations for subsequent application of REBA Sepsis-ID were 0.12 ng/mL in all patients and 0.22 ng/mL in patients aged ≥50 years. Our observations showed that REBA Sepsis-ID using whole blood was advantageous for the early detection of sepsis-causing microorganisms, and the PCT concentration could be used to determine the necessity of using REBA Sepsis-ID in clinical settings. The application of REBA Sepsis-ID using whole blood, based on the PCT concentration, may contribute to a highly efficient detection of sepsis-causing microorganisms.