Rapid and accurate detection of life-threatening microbial pathogens with high morbidity and mortality is important for the treatment of suitable antibiotics to patients with infectious diseases. Recently, DNA microarray-based identification of pathogenic microorganisms has attracted much attention from clinical researchers owing to its efficiency, specificity and reproducible high-throughput capacities, compared with conventional culture-based diagnosis, which require a long period of time for cultivation and labor-intensive assay steps. In this article, we review recently published microarray-based diagnostic studies for accurate and rapid identification of pathogens infected in bloodstream and discuss the advantages and limitations over conventional diagnostic methods.