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Children suffering from infectious diseases, both bacterial and viral, are often treated with empirical antibiotics. Keeping in mind both the menace of microorganisms and antibiotic toxicity, it is imperative to develop point-of-care testing (POCT) to discriminate bacterial from viral infections, and to define indications for antibiotic treatment. This article reviews potential protein biomarkers and host-derived gene expression signatures for differentiating between bacterial and viral infections in children, and focuses on emerging multiplex POCT devices for the simultaneous detection of sets of protein biomarkers or streamlined gene expression signatures that may provide rapid and cost-effective pathogen-discriminating tools., Highlights Bacteria and viruses activate or inhibit different signaling pathways in the cells they infect, and further give rise to different host transcriptional signatures as well as to unique protein biomarkers. Many of the newly evaluated protein biomarkers, especially in combination, have better discriminative value for distinguishing between bacterial and viral infections than the biomarkers that are currently used for examining infections in children. The transcriptomes of children undergo remarkable changes when they are infected by different types of bacteria and viruses. Approaches based on host-derived DNA/RNA signatures can accurately discriminate bacterial from viral infections. Emerging multiplex POCT techniques allow simultaneous testing of protein- or gene-based biomarkers in an outpatient setting.