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D-dimer is a widely used biomarker for the initial clinical assessment of suspected deep vein thrombosis and pulmonary embolism. Here, we presented a new fluorescence (FL) D-dimer assay system, which was developed with a platform of point-of-care test (POCT) for clinical applications.Whole blood was mixed with FL-labeled anti-D-dimer detector antibody, and then loaded onto a disposable cartridge. After 12 min of incubation, the FL intensity was acquired by scanning of test cartridge and converted as level of D-dimer in a laser FL scanner. The analytical performance of FL immunoassay was evaluated by linearity, recovery, and precision tests. The comparability of the developed assay was examined with automated reference methods.The FL assay system showed a good linearity, and the analytical mean recovery of control was 103% in a dynamic working range. The imprecision of intra- and inter-as-say of coefficient of variations from assay system was less than 8%. The developed FL assay system showed strong correlation with two automated reference assays, Vidas D-dimer (r = 0.973) and Stalia D-dimer (r = 0.971).The new FL immunoassay for D-dimer is a user-friendly, precise, and reproducible platform of POCT in whole blood.