still blood culture, this method is incapable of providing immediate results to clinicians [1] and often leads to false-negative outcomes. [2] The rapid detection and identification of bacteria in blood is vitally important because the delayed administration of antibiotics results in increased mortality [3,4] and prompt treatment of infection is frequently required for patients, particularly in emergency departments and intensive care units of hospitals. In addition, given that pathogen load is frequently proportional to patient mortality, [5] it is critical to gain quantitative information regarding the bacteria present in blood, which is still achieved largely by blood culture. While time-to-positivity (TTP) of blood cultures has been considered to be a prognostic tool for a limited range of bacterial species, such as Staphylococcus aureus (S. aureus), Escherichia coli (E. coli), and Streptococcus pneumoniae (S. pneumoniae), [6][7][8][9][10] it has not been applied more widely because correlations between TTP data for certain bacterial species and the mortality of patients was obscure in several clinical studies. [11] Despite these significant drawbacks, blood culture is still the clinical laboratory method most widely used to identify pathogenic bacteria in the blood due to the lack of appropriate, alternative approaches.Mass spectrometry (MS), [12,13] polymerase chain reaction (PCR) [14,15] and loop-mediated isothermal amplification [16] methods have all been incorporated into diagnostic procedures used for the identification of pathogenic bacteria in blood. However, they are often valid only after significant growth, in vitro, of the bacteria present in biological samples. This is often time-consuming and may not be possible, at all, for certain bacterial species due to their insufficient growth rates in standard culture conditions. Although some commercially available MS-and PCR-based diagnostic systems work directly on whole blood, eliminating the most time-consuming step of bacterial culture, [17,18] their clinical impact is still contentious due to inconsistent performance in the presence of inhibitors (e.g., human DNA, iron and heparin) and complex background signals in blood. [19] Fluorescence in situ hybridization (FISH) has permitted the unique capability in a cytogenetic analysis by using fluorescentThe current diagnosis of bacteremia mainly relies on blood culture, which is inadequate for the rapid and quantitative determination of most bacteria in blood. Here, a quantitative, multiplex, microfluidic fluorescence in situ hybridization method (μFISH) is developed, which enables early and rapid (3-h) diagnosis of bacteremia without the need for prior blood culture. This novel technology employs mannose-binding lectin-coated magnetic nanoparticles, which effectively opsonize a broad range of pathogens, magnetically sequestering them in a microfluidic device. Therein, μFISH probes, based on unique 16S rRNA sequences, enable the identification and quantification of sequestered pathogens both in saline a...